MultispeQ Beta: A tool for large-scale plant phenotyping connected to the open photosynQ network

Royal Society Open Science

Volumn 3, Issue 10, 2016, Pages

  Kuhlgert, Sebastian ^a   Austic, Greg ^a   Zegarac, Robert ^a   Osei Bonsu, Isaac ^a   Hoh, Donghee ^a   Chilvers, Martin I ^a   Roth, Mitchell G ^a   Bi, Kevin ^a   TerAvest, Dan ^a   Weebadde, Prabode ^b   Kramer, David M ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b Venturit Inc   (United States)

Author keywords

Agriculture; Chlorophyll fluorescence; Open source hardware; Phenomics; Photosynthesis

Indexed keywords

EID: 84993978164     PISSN: None     EISSN: 20545703     Source Type: Journal    
DOI: 10.1098/rsos.160592     Document Type: Article

References (57)

1. NIFA-NSF PhenomicsWorkshop Report. 2011 Phenomics: genotype to phenotype, a report of the phenomics workshop sponsored by the USDA and NSF. See http://www.nsf.gov/bio/pubs/reports/.
2. Plant Science Research Summit. 2013 Unleashing a decade of innovation in plant science: a vision for 2015-2025. See http://plantsummit.wordpress.com/.
3. Araus JL, Cairns JE. 2014 Field high-throughput phenotyping: the new crop breeding frontier. Trends Plant Sci. 19, 52-61. (doi:10.1016/j.tplants.2013. 09.008)
4. Fahlgren N, Gehan MA, Baxter I. 2015 Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Curr. Opin. Plant Biol. 24, 93-99. (doi:10.1016/j.pbi.2015.02. 006)
5. Furbank RT, Tester M. 2011 Phenomics— technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 16, 635-644. (doi:10.1016/j.tplants. 2011.09.005)
6. Ghanem ME, Marrou H, Sinclair TR. 2014 Physiological phenotyping of plants for crop improvement. Trends Plant Sci. 20, 139-144. (doi:10.1016/j.tplants.2014.11.006)
7. Granier C, Vile D. 2014 Phenotyping and beyond: modelling the relationships between traits. Curr. Opin. Plant Biol. 18, 96-102. (doi:10.1016/j.pbi. 2014.02.009)
8. White JW et al. 2012 Field-based phenomics for plant genetics research. F. Crop. Res. 133, 101-112. (doi:10.1016/j.fcr.2012.04.003)
9. Cruz JA, Savage LJ, Zegarac R, Hall CC, Satoh-Cruz M, Davis GA, Kovac WK, Chen J, Kramer DM. 2016 Dynamic environmental photosynthetic imaging reveals emergent phenotypes. Cell Syst. 2, 365-377. (doi:10.1016/j.cels.2016.06.001)
10. Kramer DM, Evans JR. 2011 The importance of energy balance in improving photosynthetic productivity. Plant Physiol. 155, 70-78. (doi:10.1104/pp.110.166652)
11. Tikkanen M, Grieco M, Nurmi M, Rantala M, Suorsa M, Aro E-M. 2012 Regulation of the photosynthetic apparatus under fluctuating growth light. Phil. Trans. R. Soc. B 367, 3486-3493. (doi:10.1098/rstb. 2012.0067)
12. Hüner NPA, Dahal K, Bode R, Kurepin LV, Ivanov AG. 2016 Photosynthetic acclimation, vernalization, crop productivity and ‘the grand design of photosynthesis. J. Plant Physiol. (doi:10.1016/j.jplph.2016. 04.006)
13. Peterson RKD, Higley LG. 2001 Biotic Stress and Yield Loss (eds R Peterson, L Higley). Boca Raton, FL: CRC Press.
14. Mochida K, Saisho D, Hirayama T. 2015 Crop improvement using life cycle datasets acquired under field conditions. Front. Plant Sci. 6, 740. (doi:10.3389/fpls.2015.00740)
15. Allahverdiyeva Y, Suorsa M, Tikkanen M, Aro EM. 2015 Photoprotection of photosystems in fluctuating light intensities. J. Exp. Bot. 66, 2427-2436. (doi:10.1093/jxb/eru463)
16. Baker NR, Harbinson J, Kramer DM. 2007 Determining the limitations and regulation of photosynthetic energy transduction in leaves. Plant. Cell Environ. 30, 1107-1125. (doi:10.1111/j.1365-3040. 2007.01680.x)
17. Apel K, Hirt H. 2004 Reactive oxygen species: metabolism, oxidative stress, signal transduction. Annu. Rev. Plant Biol. 55, 373-399. (doi:10.1146/annurev.arplant.55.031903.141701)
18. Cooper CB, Shirk J, Zuckerberg B. 2014 The invisible prevalence of citizen science in global research: migratory birds and climate change. PLoS ONE 9, e106508. (doi:10.1371/journal.pone.0106508)
19. Silvertown J. 2009 A new dawn for citizen science. Trends Ecol. Evol. 24, 467-471. (doi:10.1016/j.tree. 2009.03.017)
20. Bonney R, Ballard H, Jordan R, McCallie E, Phillips T, Shirk J, Wilderman CC. 2009 Public participation in scientific research: Defining the field and assessing its potential for informal science education. A CAISE Inquiry Group Report.Washington DC: Center for Advancement of Informal Science Education (CAISE).
21. Droege S. 2007 Just because you paid them doesn’t mean their data are better. In Citizen Science Toolkit Conference (eds CM In, R Bonney, J Dickinson, S Kelling, K Rosenberg, J Shirk), pp. 1-14. Ithaca, NY.
22. Worthington JP, Silvertown J, Cook L, Cameron R, Dodd M, Greenwood RM, McConway K, Skelton P. 2012 Evolution MegaLab: a case study in citizen science methods. Methods Ecol. Evol. 3, 303-309. (doi:10.1111/j.2041-210X.2011.00164.x)
23. Davies L et al. 2011 Open air laboratories (OPAL): a community-driven research programme. Environ. Pollut. 159, 2203-2210. (doi:10.1016/j.envpol. 2011.02.053)
24. Bhattacharjee Y. 2005 Ornithology. Citizen scientists supplement work of Cornell researchers. Science 308, 1402-1403. (doi:10.1126/science.308.5727. 1402)
25. Ruby S, Thomas D, Hansson DH. 2013 AgileWeb Development with Rails 4 (ed. SD Pfalzer), 1st edn. Pragmatic Bookshelf.
26. Culman SW, Snapp SS, Green JM, Gentry LE. 2013 Short-and long-term labile soil carbon and nitrogen dynamics reflect management and predict corn agronomic performance. Agron. J. 105, 493-502. (doi:10.2134/agronj2012.0382)
27. Xiong D, Chen J, Yu T, Gao W, Ling X, Li Y, Peng S, Huanga J. 2015 SPAD-based leaf nitrogen estimation is impacted by environmental factors and crop leaf characteristics. Sci. Rep. 5, 13389. (doi:10.1038/srep13389)
28. de Andrade SAL, Domingues AP, Mazzafera P. 2015 Photosynthesis is induced in rice plants that associate with arbuscular mycorrhizal fungi and are grown under arsenate and arsenite stress. Chemosphere 134, 141-149. (doi:10.1016/j. chemosphere.2015.04.023)
29. Markwell J, Osterman JC, Mitchell JL. 1995 Calibration of the Minolta SPAD-502 leaf chlorophyll meter. Photosynth. Res. 46, 467-472. (doi:10.1007/BF00032301)
30. Baker NR, Rosenqvist E. 2004 Applications of chlorophyll fluorescence can improve crop production strategies: an examination of future possibilities. J. Exp. Bot. 55, 1607-1621. (doi:10.1093/jxb/erh196)
31. Baker NR. 2008 Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annu. Rev. Plant Biol. 59, 89-113. (doi:10.1146/annurev.arplant.59.032607. 092759)
32. Genty B, Briantais J-M, Baker NR. 1989 The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochim. Biophys. Acta Gen. Subj. 990, 87-92. (doi:10.1016/S0304-4165(89) 80016-9)
33. Cazzaniga S, Dall’ Osto L, Kong S-G, Wada M, Bassi R. 2013 Interaction between avoidance of photon absorption, excess energy dissipation and zeaxanthin synthesis against photooxidative stress in Arabidopsis. Plant J. 76, 568-579. (doi:10.1111/tpj.12314)
34. Dutta S, Cruz JA, Jiao Y, Chen J, Kramer DM, Osteryoung KW. 2015 Non-invasive, whole-plant imaging of chloroplast movement and chlorophyll fluorescence reveals photosynthetic phenotypes independent of chloroplast photorelocation defects in chloroplast division mutants. Plant J. 84, 428-442. (doi:10.1111/tpj.13009)
35. Kramer DM, Johnson G, Kiirats O, Edwards GE. 2004 New fluorescence parameters for the determination of QA redox state and excitation energy fluxes. Photosynth. Res. 79, 209-218. (doi:10.1023/B:PRES. 0000015391.99477.0d)
36. Kramer D, Cruz J, Hall C, Kovac WK, Zegarac R. 2013 Plant phenometrics systems and methods and devices related thereto. See http://www.google.com/patents/WO2013181433A2?cl=en.
37. Junge W, Witt HT. 1969 Analysis of electrical phenomena in membranes and interfaces by absorption changes. Nature 222, 1062-1062. (doi:10.1038/2221062a0)
38. Cruz JA, Sacksteder CA, Kanazawa A, Kramer DM. 2001 Contribution of electric field (Delta psi) to steady-state transthylakoid proton motive force (pmf) in vitro and in vivo. Control of pmf parsing into Delta psi and Delta pH by ionic strength. Biochemistry 40, 1226-1237. (doi:10.1021/bi0018 741)
39. Kanazawa A, Kramer DM. 2002 In vivo modulation of nonphotochemical exciton quenching (NPQ) by regulation of the chloroplast ATP synthase. Proc. Natl Acad. Sci. USA 99, 12 789-12 794. (doi:10.1073/pnas.182427499)
40. Kohzuma K, Cruz JA, Akashi K, Hoshiyasu S, Munekage YN, Yokota A, Kramer DM. 2009 The long-term responses of the photosynthetic proton circuit to drought. Plant. Cell Environ. 32, 209-219. (doi:10.1111/j.1365-3040.2008.01912.x)
41. Livingston AK, Kanazawa A, Cruz JA, Kramer DM. 2010 Regulation of cyclic electron flow in C3 plants: differential effects of limiting photosynthesis at ribulose-1,5-bisphosphate carboxylase/oxygenase and glyceraldehyde-3-phosphate dehydrogenase. Plant. Cell Environ. 33, 1779-1788. (doi:10.1111/j.1365-3040.2010.02183.x)
42. Bailleul B, Cardol P, Breyton C, Finazzi G. 2010 Electrochromism: a useful probe to study algal photosynthesis. Photosynth. Res. 106, 179-189. (doi:10.1007/s11120-010-9579-z)
43. Kohzuma K, Dal Bosco C, Meurer J, Kramer DM. 2013 Light-andmetabolism-related regulation of the chloroplast ATP synthase has distinct mechanisms and functions. J. Biol. Chem. 288, 13156-13163. (doi:10.1074/jbc.M113.453225)
44. Kohzuma K, Dal Bosco C, Kanazawa A, Dhingra A, Nitschke W, Meurer J, Kramer DM. 2012 Thioredoxin-insensitive plastid ATP synthase that performs moonlighting functions. Proc. Natl Acad. Sci. USA 109, 3293-3298. (doi:10.1073/pnas.1115 728109)
45. Sacksteder CA, Kramer DM. 2000 Dark-interval relaxation kinetics (DIRK) of absorbance changes as a quantitative probe of steady-state electron transfer. Photosynth. Res. 66, 145-158. (doi:10.1023/A:1010785912271)
46. Sacksteder CA, Jacoby ME, Kramer DM. 2001 A portable, non-focusing optics spectrophotometer (NoFOSpec) for measurements of steady-state absorbance changes in intact plants. Photosynth. Res. 70, 231-240. (doi:10.1023/A:1017906 626288)
47. Hall C, Cruz J, Wood M, Zegarac R, DeMars D, Carpenter J, Kanazawa A, Kramer D. 2013 Photosynthetic measurements with the Idea Spec: an integrated diode emitter array spectrophotometer/fluorometer. Photosynth. Res. Food Fuel Futur. 184-188. (doi:10.1007/978-3-642-32034-7_38)
48. Avenson TJ, Cruz JA, Kanazawa A, Kramer DM. 2005 Regulating the proton budget of higher plant photosynthesis. Proc. Natl Acad. Sci. USA 102, 9709-9713. (doi:10.1073/pnas.0503952102)
49. Walker BJ, Strand DD, Kramer DM, Cousins AB. 2014 The response of cyclic electron flowaround photosystem I to changes in photorespiration and nitrate assimilation. Plant Physiol. 165, 453-462. (doi:10.1104/pp.114.238238)
50. Cruz JA, Avenson TJ, Kanazawa A, Takizawa K, Edwards GE, Kramer DM. 2005 Plasticity in light reactions of photosynthesis for energy production and photoprotection. J. Exp. Bot. 56, 395-406. (doi:10.1093/jxb/eri022)
51. Kiirats O, Kramer DM, Edwards GE. 2010 Co-regulation of dark and light reactions in three biochemical subtypes of C4 species. Photosynth. Res. 105, 89-99. (doi:10.1007/s11120-010-9561-9)
52. Schöttler MA, Flügel C, Thiele W, Stegemann S, Bock R. 2007 The plastome-encoded PsaJ subunit is required for efficient Photosystem I excitation, but not for plastocyanin oxidation in tobacco. Biochem. J. 403, 251-260. (doi:10.1042/BJ20061573)
53. Aoki T, O’Donnell K, Homma Y, Lattanzi AR. 2003 Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within the Fusarium solani species complex—F. virguliforme in North America and F. tucumaniae in South America. Mycologia 95, 660-684. (doi:10.2307/3761942)
54. Fehr WR, Caviness CE, Burmood DT, Pennington JS. 1971 Stage of development descriptions for soybeans, Glycinemax (L.) Merrill. Crop Sci. 11, 929-931. (doi:10.2135/cropsci1971.0011183X00 1100060051x)
55. Ji J, Scott MP, Bhattacharyya MK. 2006 Light is essential for degradation of ribulose-1,5-bisphosphate carboxylase-oxygenase large subunit during sudden death syndrome development in soybean. Plant Biol. 8, 597-605. (doi:10.1055/s-2006-924175)
56. Gholizadeh A, Amin MSM, Anuar AR, Aimrun W. 2009 Evaluation of SPAD chlorophyll meter in two different rice growth stages and its temporal variability. Eur. J. Sci. Res. 37, 591-598.
57. Hörtensteiner S, Kräutler B. 2011 Chlorophyll breakdown in higher plants. Biochim. Biophys. Acta Bioenerg. 1807, 977-988. (doi:10.1016/j.bbabio. 2010.12.007)