Towards an understanding of root system wide integration of environmental cues

XVI Congreso Nacional de Bioquímica y Biología Molecular de Plantas y 9th Symposium México-USA. Querétaro Dec-2015
Here we propose a framework for analysis of root system architecture, gene expression and soil properties to leverage the development of tools that allow integration of these multidimensional information to better understand how roots are able to adapt root function and shape to heterogeneous spatial environmental cues.

Transcript

1. Towards an understanding of root system wide integration of environmental cues ubén Rellán Álvarez @rubenrellan rrellan@langebio.cinvestav.mx www.rrlab.org bit.ly/goo-roots-paper bit.ly/SMB-2015-slides www.rrlab.org/GLO-Roots
2. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/ water Phosphate Roots integrate a variety of signals and adjust function and shape accordingly
3. Drew et al. 1978 JXB 109:435 High N Low N
4. A B C D E Contact Air lateral root aerenchyma aerenchyma lateral root macro- pore Soil macro- pore Soil Rellán-Álvarez, Lobet & Dinneny 2015 In Press Figure credit S. Mooney, C Sturrock, N. Robbins & J. Dinneny Roots integrate a variety of signals and adjust function and shape accordingly
5. low N high N CEP1 LRR-RK CK CLE3-CLV1 NRT1.1 Auxin NRT1.1 Auxin N03 - ? HRS1 low P HRS1 NRT1.1 How can roots integrate & regulate local clues with whole root system responses? Adapted from Rellán-Álvarez, Lobet & Dinneny 2015 In Press Krouk et al 2010 PMID 20627075 Medici et al 2015 PMID 25723764 Ruffel et al 2011 PMID 22025711 Tabata et al. 2014 PMID: 25324386 Araya et al 2014 PMID 24449877
6. Yun et al. 2014 PMID: 24927545 From metabolite in vivo imaging to 3D in soil root architecture Grossman et al. 2011 PMID: 22186371 Soil Artificial Substrate
7. Yun et al. 2014 PMID: 24927545 From metabolite in vivo imaging to 3D in soil root architecture Grossman et al. 2011 PMID: 22186371 Soil Artificial Substrate
8. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression We designed a root imaging system able to integrate different types of information Growth and Luminescence Observatory for Roots
9. Transpiring environment Roots protected from light
10. 30 cm 15 cm 2 mm 100 cm3 of soil Rhizotrons: a 2D sample of soil
11. 30 cm 15 cm 2 mm 100 cm3 of soil Rhizotrons: a 2D sample of soil
12. Rhizotrons: a 2D sample of soil
13. Rhizotrons allow normal plant growth
14. Roots grown in rhizotrons are similar to roots grown in pots Fresh Weight FW (mg) 0 60 120 180 240 MS Pot Rhizotron
15. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/ water Phosphate
16. Different environmental cues can be recreated and quantified in rhizotrons water
17. Different environmental cues can be recreated and quantified in rhizotrons water
18. Different environmental cues can be recreated and quantified in rhizotrons water
19. Different environmental cues can be recreated and quantified in rhizotrons water Soil Moisture (%) 0 20 40 60 80 mean intensity 36 40 44 48 52 y = -0.0564x2 + 1.0466x + 111.09 y = -3.96x + 220.8 R2 = 0.88
20. Different environmental cues can be recreated and quantified in rhizotrons water Soil Moisture (%) 0 20 40 60 80 mean intensity 36 40 44 48 52 y = -0.0564x2 + 1.0466x + 111.09 y = -3.96x + 220.8 R2 = 0.88
21. Different environmental cues can be recreated and quantified in rhizotrons water Phosphate Soil Moisture (%) 0 20 40 60 80 mean intensity 36 40 44 48 52 y = -0.0564x2 + 1.0466x + 111.09 y = -3.96x + 220.8 R2 = 0.88
22. Different environmental cues can be recreated and quantified in rhizotrons water Phosphate Soil Moisture (%) 0 20 40 60 80 mean intensity 36 40 44 48 52 y = -0.0564x2 + 1.0466x + 111.09 y = -3.96x + 220.8 R2 = 0.88
23. Different environmental cues can be recreated and quantified in rhizotrons water Phosphate Soil Moisture (%) 0 20 40 60 80 mean intensity 36 40 44 48 52 y = -0.0564x2 + 1.0466x + 111.09 y = -3.96x + 220.8 R2 = 0.88
26. We use luciferase to visualize roots in soil www.firefly.org/firefly-pictures.html Luciferase is great! •Does not require any light excitation •No background luminescence •LUC can be used in temporal studies •Dynamic response to gene expression •Multiple color reporters are possible luciferin + ATP + O2 → oxyluciferin +
27. Prom mCherry Luciferase 35S Emami et al. 2013 PMID: 24032037 Although we are also exploring the use of fluorescent proteins
28. Prom mCherry Luciferase 35S Emami et al. 2013 PMID: 24032037 Although we are also exploring the use of fluorescent proteins
29. Prom mCherry Luciferase 35S Emami et al. 2013 PMID: 24032037 Although we are also exploring the use of fluorescent proteins
30. Although we are also exploring the use of fluorescent proteins
31. Although we are also exploring the use of fluorescent proteins
32. Roots are visualized with the GLO1 imaging system
33. Roots are visualized with the GLO1 imaging system
34. Both sides of the rhizotron are combined visualize the full root system ProUBQ10:LUC2o
35. Both sides of the rhizotron are combined visualize the full root system ProUBQ10:LUC2o
36. Images are data
37. Images are data
38. And there is a lot of data that can be gathered from this type of images DAS 0 21
39. GLO-RIA is an ImageJ plugin developed to analyze GLO-Roots images bit.ly/GLO-RIA www.guillaumelobet.be
40. 11 12 13 14 15 16 17 18 19 20 21 GLO-RIA enables semi-automatic quantification of RSA traits
41. GLO-RIA enables semi-automatic quantification of RSA traits 11 12 13 14 15 16 17 18 19 20 21
42. GLO-RIA enables semi-automatic quantification of RSA traits 11 12 13 14 15 16 17 18 19 20 21 Count 0 45 90 Count 0 45 90 Count 0 45 90
43. GLO-RIA enables semi-automatic quantification of RSA traits 11 12 13 14 15 16 17 18 19 20 21 Angle Count 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90
44. Low Light RSA (cm2) 0 100 200 300 400 Days After Sowing 10 20 30 40 50 23 DAS 33 DAS High Light
45. Different accessions show distinct root traits including lateral root angle
46. Different accessions show distinct root traits including lateral root angle
47. Root system architecture is light regulated
48. Root system architecture is light regulated
49. Root system architecture is light regulated
50. Root system architecture is light regulated
51. Several degrees of water deficit can be induced
52. Several degrees of water deficit can be induced
53. Early withdrawal of water may affect lateral root emergence
54. Early withdrawal of water may affect lateral root emergence
55. Early withdrawal of water may affect lateral root emergence
56. Early withdrawal of water may affect lateral root emergence
57. + 24 h Early withdrawal of water may affect lateral root emergence
58. If water deprivation starts later there is an induction of lateral root growth and a higher proliferation of tertiary roots
59. Lateral root angle is affected differently in different ecotypes in response to water deprivation
60. Root direction correlates with local soil moisture content WW WD
61. 500 540 580 620 660 700 UBQ10:vLUC2 ACT2:PpyREo We have generated a golden gate ready collection of different luciferases Intensity 1005 1064 1123 1182 1241 1300 UBQ10:CBRo Intensity 1005 1064 1123 1182 1241 1300 500 540 580 620 660 700 UBQ10:LUC2o 500 540 580 620 660 700 UBQ10:CBGo LUC2o Maximum Intensity vLUC CBG99o PpyRE8o CBRo λ (nm)
62. Plant-plant and plant-microbe interactions imaged using different luciferases
63. Simultaneous imaging of root structure and gene is expression is possible Open 517-567 nm Merged ProACT2:PPyRE8o x ProZat12:LUC
64. We can seamlessly integrate different types of information at the whole root system level Figure credit: Guillaume Lobet Rellán-Álvarez, Lobet & Dinneny 2015 In Press
65. And then use this information to understand and model root architecture and function using functional structural models Adapted from Lobet et al 2015 PMID: 25614065 Root System Markup Language 1 2 3 4 5 Topology nested document structure Geometry polyline representation Functions associated with polyline - diameter - age - gene expression - … Low N High N Adapted from Rellán-Álvarez, Lobet & Dinneny 2015 In Press
66. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression A multidimensional map of root responses to soil environmental cues
67. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression A multidimensional map of root responses to soil environmental cues
69. Dinneny Lab Muh-Ching Yee Geng Yu Emilie Winfield Pierre-Luc Pradier Charlotte Trontin Thérèse LaRue Heike Lindner Guillaume Lobet Root Image Analysis and root modelling Jose Sebastian John Vogel Julin Maloof Other Species Cara Haney
70. CINVESTAV
71. Root system wide integration of environmental cues Phospholipid role in plant adaptation to low P and high altitude www.rrlab.org#projects
72. Courtesy of Charlotte Trontin
73. Towards an understanding of root system wide integration of environmental cues ubén Rellán Álvarez @rubenrellan rrellan@langebio.cinvestav.mx www.rrlab.org bit.ly/goo-roots-paper bit.ly/SMB-2015-slides www.rrlab.org/GLO-Roots