Germinator: A software package for high-throughput scoring and curve fitting of Arabidopsis seed germination

Plant Journal

Volumn 62, Issue 1, 2010, Pages 148-159

  Joosen, Ronny V L ^a   Kodde, Jan ^a   Willems, Leo A J ^a   Ligterink, Wilco ^a   Van Der Plas, Linus H W ^a   Hilhorst, Henk W M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Arabidopsis; Automated scoring; Curve fitting; Germination; Image analysis

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS SEEDS; ARABIDOPSIS THALIANA; AUTOMATED SCORING; BRASSICA; COLOR CONTRAST; COST-EFFICIENT; EXPERIMENTAL SETUP; GERMINATION TEST; HIGH QUALITY; HIGH-THROUGHPUT; LARGE POPULATION; NATURAL VARIATION; PLANT SPECIES; QUANTITATIVE TRAIT LOCUS; RECOMBINANT INBRED LINES; REPRODUCIBILITIES; SALT TOLERANCE; SCIENTIFIC DISCOVERY; SCORING SYSTEMS; SEED COATS; SEED PHYSIOLOGY; SINGLE IMAGES;

DATA VISUALIZATION; IMAGE ANALYSIS; PACKAGING; PLANTS (BOTANY); SEED; VISUALIZATION;

CURVE FITTING;

ARABIDOPSIS; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENETICS; GERMINATION; HALOPHYTE; IMAGE PROCESSING; PHYSIOLOGY; PLANT SEED; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY;

ARABIDOPSIS; GENE EXPRESSION REGULATION, PLANT; GERMINATION; IMAGE PROCESSING, COMPUTER-ASSISTED; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; SALT-TOLERANT PLANTS; SEEDS; SOFTWARE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICA;

EID: 77951799002     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2009.04116.x     Document Type: Article

References (38)

1. Baecker, P. Travo, P. (2006) Cell image analyzer: a visual scripting interface for ImageJ and its usage at the microscopy facility Montpellier RIO. Proc. ImageJ User Developer Conf. 1, 105 110.
2. Bentsink, L., Alonso-Blanco, C., Vreugdenhil, D., Tesnier, K., Groot, S.P.C. Koornneef, M. (2000) Genetic analysis of seed-soluble oligosaccharides in relation to seed storability of Arabidopsis. Plant Physiol. 124, 1595 1604.
3. Bewley, J.D. (1997) Seed germination and dormancy. Plant Cell, 9, 1055 1066.
4. Brown, R.F. Mayer, D.G. (1988) Representing cumulative germination. 2. The use of the Weibull function and other empirically derived curves. Ann. Bot. 61, 127 138.
5. Cadman, C.S.C., Toorop, P.E., Hilhorst, H.W.M. Finch-Savage, W.E. (2006) Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. Plant J. 46, 805 822.
6. Clerkx, E.J.M., El-Lithy, M.E., Vierling, E., Ruys, G.J., Blankestijn-De Vries, H., Groot, S.P.C., Vreugdenhil, D. Koornneef, M. (2004) Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landsberg erecta and Shakdara, using a new recombinant inbred line population. Plant Physiol. 135, 432 443.
7. Dell'Aquila, A. (2004) Cabbage, lentil, pepper and tomato seed germination monitored by an image analysis system. Seed Sci. Technol. 32, 225 229.
8. Dell'Aquila, A. (2005) The use of image analysis to monitor the germination of seeds of broccoli (Brassica oleracea) and radish (Raphanus sativus). Ann. Appl. Biol. 146, 545 550.
9. Dell'Aquila, A. (2007) Pepper seed germination assessed by combined X-radiography and computer-aided imaging analysis. Biol. Plant. 51, 777 781.
10. Dell'Aquila, A. (2009) Digital imaging information technology applied to seed germination testing. A review. Agron. Sustain. Develop. 29, 213 221.
11. Dell'Aquila, A., Van Eck, J.W. Van Der Heijden, G.W.A.M. (2000) The application of image analysis in monitoring the imbibition process of white cabbage (Brassica oleracea L.) seeds. Seed Sci. Res. 10, 163 169.
12. Ducournau, S., Feutry, A., Plainchault, P., Revollon, P., Vigouroux, B. Wagner, M.H. (2005) Using computer vision to monitor germination time course of sunflower (Helianthus annuus L.) seeds. Seed Sci. Technol. 33, 329 340.
13. El-Kassaby, Y.A., Moss, I., Kolotelo, D. Stoehr, M. (2008) Seed germination: mathematical representation and parameters extraction. Forest Sci. 54, 220 227.
14. Espinosa-Ruiz, A., Bellés, J.M., Serrano, R. Culiáñ ez-Macià, F.A. (1999) Arabidopsis thaliana AtHAL3: a flavoprotein related to salt and osmotic tolerance and plant growth. Plant J. 20, 529 539.
15. Finch-Savage, W.E. Leubner-Metzger, G. (2006) Seed dormancy and the control of germination. New Phytol. 171, 501 523.
16. Gallardo, K., Job, C., Groot, S.P.C., Puype, M., Demol, H., Vandekerckhove, J. Job, D. (2001) Proteomic analysis of Arabidopsis seed germination and priming. Plant Physiol. 126, 835 848.
17. Goda, H., Sasaki, E., Akiyama, K. et al. (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J. 55, 526 542.
18. Hobbs, D.H., Flintham, J.E. Hills, M.J. (2004) Genetic control of storage oil synthesis in seeds of Arabidopsis. Plant Physiol. 136, 3341 3349.
19. Hong, S.W. Vierling, E. (2000) Mutants of Arabidopsis thaliana defective in the acquisition of tolerance to high temperature stress. Proc. Natl Acad. Sci. USA, 97, 4392 4397.
20. Khajeh-Hosseini, M., Lomholt, A. Matthews, S. (2009) Mean germination time in the laboratory estimates the relative vigour and field performance of commercial seed lots of maize (Zea mays L.). Seed Sci. Technol. 37, 446 456.
21. Kim, Y.O., Kim, J.S. Kang, H. (2005) Cold-inducible zinc finger-containing glycine-rich RNA-binding protein contributes to the enhancement of freezing tolerance in Arabidopsis thaliana. Plant J. 42, 890 900.
22. Kliebenstein, D.J., Gershenzon, J. Mitchell-Olds, T. (2001) Comparative quantitative trait loci mapping of aliphatic, indolic and benzylic glucosinolate production in Arabidopsis thaliana leaves and seeds. Genetics, 159, 359 370.
23. Leon-Kloosterziel, K.M., van de Bunt, G.A., Zeevaart, J.A. Koornneef, M. (1996) Arabidopsis mutants with a reduced seed dormancy. Plant Physiol. 110, 233 240.
24. Lin, Y., Sun, L., Nguyen, L.V., Rachubinski, R.A. Goodman, H.M. (1999) The Pex16p homolog SSE1 and storage organelle formation in Arabidopsis seeds. Science, 284, 328 330.
25. Liu, P.P., Koizuka, N., Homrichhausen, T.M., Hewitt, J.R., Martin, R.C. Nonogaki, H. (2005) Large-scale screening of Arabidopsis enhancer-trap lines for seed germination-associated genes. Plant J. 41, 936 944.
26. Lou, P., Zhao, J., He, H., Hanhart, C., Del Carpio, D.P., Verkerk, R., Custers, J., Koornneef, M. Bonnema, G. (2008) Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves. New Phytol. 179, 1017 1032.
27. Loudet, O., Chaillou, S., Camilleri, C., Bouchez, D. Daniel-Vedele, F. (2002) Bay-0 × Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theor. Appl. Genet. 104, 1173 1184.
28. Muller, K., Tintelnot, S. Leubner-Metzger, G. (2006) Endosperm-limited Brassicaceae seed germination: abscisic acid inhibits embryo-induced endosperm weakening of Lepidium sativum (cress) and endosperm rupture of cress and Arabidopsis thaliana. Plant Cell Physiol. 47, 864 877.
29. Munnik, T., Ligterink, W., Meskiene, I., Calderini, O., Beyerly, J., Musgrave, A. Hirt, H. (1999) Distinct osmo-sensing protein kinase pathways are involved in signalling moderate and severe hyper-osmotic stress. Plant J. 20, 381 388.
30. Penfield, S. King, J. (2009) Towards a systems biology approach to understanding seed dormancy and germination. Proc. R. Soc. B: Biol. Sci. 276, 3561 3569.
31. Quesada, V., García-Martínez, S., Piqueras, P., Ponce, M.R. Micol, J.L. (2002) Genetic architecture of NaCl tolerance in Arabidopsis. Plant Physiol. 130, 951 963.
32. Routaboul, J.M., Kerhoas, L., Debeaujon, I., Pourcel, L., Caboche, M., Einhorn, J. Lepiniec, L. (2006) Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Planta, 224, 96 107.
33. Schaar, W.V.D., Alonso Blanco, C., Leon Kloosterziel, K.M., Jansen, R.C., Ooijen, J.W.V. Koornneef, M. (1997) QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping. Heredity, 79, 190 200.
34. Shirley, B.W., Kubasek, W.L., Storz, G., Bruggemann, E., Koornneef, M., Ausubel, F.M. Goodman, H.M. (1995) Analysis of Arabidopsis mutants deficient in flavonoid biosynthesis. Plant J. 8, 659 671.
35. Teixeira, P.C.N., Coelho Neto, J.A., Rocha, H. De Oliveira, J.M. (2007) An instrumental set up for seed germination studies with temperature control and automatic image recording. Braz. J. Plant Physiol. 19, 99 108.
36. Vreugdenhil, D., Aarts, M.G.M., Koornneef, M., Nelissen, H. Ernst, W.H.O. (2004) Natural variation and QTL analysis for cationic mineral content in seeds of Arabidopsis thaliana. Plant Cell Environ. 27, 828 839.
37. Wehmeyer, N. Vierling, E. (2000) The expression of small heat shock proteins in seeds responds to discrete developmental signals and suggests a general protective role in desiccation tolerance. Plant Physiol. 122, 1099 1108.
38. Zhu, J.K. (2002) Salt and drought stress signal transduction in plants. Annu. Rev. Plant Biol. 53, 247 273.