Plant Phenomics

Recent Progresses in Plant Phenomics

1. RECENT PROGRESSES IN PLANT PHENOMICS Navaneetha Krishnan J L-2016-A-18-D School of Agricultural Biotechnology Punjab Agricultural University Ludhiana

2. SEMINAR OUTLINE

3. Wild Ancestors of Some Crops https://i0.wp.com/www.exposingtruth.com/wpcontent/uploads/2015/03/originalfoods.png?resize=452%2C497 https ://pbs.twimg.com/media/C-Qe026WsAEfGQY.jpg INTRODUCTION

4. Genotype and Phenotype Wilhelm Johannsen (1857–927) Johannsen (1903)

5. Plant Phenomics , Phenome and Phene

6. The P henotpying B ottleneck https://genome.duke.edu/sites/genome.duke.edu/files/ngs_slide6.jpg Genomic Selection Genotyping by Sequencing GWAS Next Generation S equencing High- thoughput Genotyping SNP chips High-throughput Phenotyping https:// www.olympusims.com/data/Imge/appnotes/data_collections_xrf_field_china.JPG?rev=9ECF http:// hibusiness.ca/wpcontent/uploads/2017/06/snail-graph-slow.jpg Spatial and temporal flexibility Time consuming Labour intensive Conventional Phenotyping

7. Levels of Plant P henotyping and Factors Influencing the Phenotype Dhondt S et al (2013) Trends Plant Sci 18 :428-39

8. Forward and Reverse Phenomics Kumar J et al (2015) Phenomics in Crop Plants: Trends, Options and Limitations Springer, India pp. (1-10)

9. Controlled Environment vs Field Phenotyping Controlled Environment Field Better control of soil moisture and nutrient inputs Difficult to control input application Offseason phenotyping and imposition of biotic stress possible Not possible Accurate data acquisition under desired lighting using variety of cameras Lighting cannot be controlled, shadow effects and influence of wind Cannot immitate natural field conditons -space constraints Natural growth environment of the crop Two approaches : Moving plants along the sensors and Moving sensors along the plants Single approach : Moving sensors along the plants

10. Phenotyping Technologies and Platforms

11. Variety of Imaging Cameras Fahlgren N et al (2015) Curr Opin Plant Biol 24 : 93-99

12. Imaging technologies

13. Golzarian M R et al (2011) Plant Methods 7 :2 Image processing steps used in the extraction of plant's projected shoot area from 2D visual images (1) Visible l ight imaging

14. C omparison of LAI measured by the LAI-2000 and derived from digital colour photographs Liu J and Pattey E (2010) Agric For Meteorol 150 :1485-90

15. (2) Thermal Imaging Thermal imaging allows for the visualization of infrared radiation, indicating an object as the temperature across the object’s surface Furbank R T and Tester M (2011) Trends Plant Sci   16 : 635-44

16. (3) Spectral imaging http://gisgeography.com/multispectral-vs-hyperspectral-imagery-explained/ Two types:

17. Barbagallo R P et al (2003) Plant Physiol   132 : 485-93 (4) Flourescence imaging

18. Images of standard mock control and Dickeya dadantii -infected zucchini leaves at 3, 7 and 10 days post inoculation (dpi )

19. (5) 3-Dimensional imaging Paulus S et al ( 2014) Biosyst Eng 121 :1-11

20. Overview of 3D scanning and reconstruction process Nguyen C et al (2016) In   Digital Image Computing: Techniques and Applications (DICTA), 2016 International Conference on   IEEE pp . 1-8

21. 6) Magnetic Resonance Imaging (MRI) M aize plant at 10 DAS Dusschoten D V et al (2016) Plant Physiol doi : 10.1104/pp.15.01388

22. 7) X-ray computed tomography http:// www.shimadzu.com/an/sites/default/files/ckeditor/an/ndi/ct/qn5042000002jzy4img/qn5042000002k8hg.jpg 3-D visualization of maize roots Mooney S J et al 2012 Plant Soil 352 :1–22

23.  X-ray Computed Tomography system at the Danforth Plant Science Center, Missouri https://www.danforthcenter.org/news-media/roots-shoots-blog/blog-item/unique-imaging-platform-to-advance-research-on-the-development-of-roots

24. PHENOTYPING PLATFORMS

25. Controlled Environment Phenotyping Platforms LemnaTec , Germany http://www.lemnatec.com/products/

26. Phenospex , Netherlands PlantEye F500 https://phenospex.com/products/plant-phenotyping/science-planteye-3d-laser-scanner/ planteye-f500-multispectral-3d-laser-scanner /

27. DroughtSpotter https://phenospex.com/products/plant-phenotyping/drought-control-platform/

28. Field Scanalyzer ( LemnaTec ) http://www.lemnatec.com/products/ Ground-based Plant Phenotyping Platforms

29. Plant Phenotyping system built on a open rider sprayer sonar proximity sensor/ infrared radiometer sensor multi-spectral crop canopy sensor Andrade-Sanchez P et al (2014) Funct Plant Biol 41 : 68-79 GPS-RTK receiver-antenna

30. Rebetzke G J et al (2013) Funct Plant Biol 40 :1-13 Purpose built crop monitoring buggy

31. Aerial Phenotyping Watanabe K et al (2017) Front Plant Sci 8 doi : 10.3389/fpls.2017.00421 Unmanned Aerial Vehicle (UAV) based phenotyping

32. Phenocopter Chapman S C et al (2014) Agronomy 4 (2 ):279-301

33. Phenotyping the hidden half Root Phenotyping http:// www.barleyhub.org/wordpress/wpcontent/uploads/2016/10/3.jpg

34. S. No Plant Cultivation System Growth Media 1. Magnetic resonance imaging Soil (lab, greenhouse and field) 2. X-Ray computed tomography Soil ( lab, greenhouse and field) 3 . Rhizoponics Liquid media (lab) 4 . Clear pot method Soil (greenhouse) 5. Shovelomics Soil (field-based) 6. Soil coring Soil (field-based) 7. Rhizolysimeters Soil (field-based) 8. Minirhizotrons Soil (field-based) Paez -Garcia A et al ( 2015) Plants   4 : 334-55 Approaches for Root Phenotyping

35. Mathew L et al ( 2015) Plant methods 11 : 3 Rhizoponics https://grdc.com.au/~/media/images/ground-cover/ground-cover-127-supplement/p12-13_figure-2_clear-pots1.jpg Clear pot method Soil filled rhizotrons https://www.pfluglos.de/nachrichten/wurzelforschung-eine-neue-aufgabe-fuer-die-pflanzenzuechtung

36. Rhizolysimeters Eberbach P et al (2006) Campbell Scientific Inc , USA Minirhizotrons Johnson M G et al (2001) Environ Exper Bot 45 :263-289

37. Pask A J D et al (2012) Physiological breeding II: a field guide to wheat phenotyping . Cimmyt pp. (87-94) Soil coring http://research.ncl.ac.uk/nefg/nuecrops/n7.php Shovelomics

38. Jeudy C   et al (2016) Plant methods   12 :31 Rhizotubes

39. Root image analysis Software packages for imaging roots and extracting quantitative data from captured root images RootScan RootNav , DART GiARoots IJ Rhizo , RootSystemAnalyzer RootReader RootReader3D RooTrak The method for culturing the plants often dictates the usefulness of a particular image analysis tool Paez -Garcia A et al ( 2015) Plants   4: 334-55

40. Data Integration in Plant Phenomics M ulti-trait phenotyping pipeline Granier C and Vile D (2014) Curr Opin Plant Biol 18 : 96-102

41. Rahaman M M et al (2015) Front Plant Sci 6 :619 doi : 10.3389/fpls.2015.00619 High-throughput plant phenotyping and data accumulation

42. Online tools for Plant Phenomics

43. Plant Image Analysis http://www.plant-image-analysis.org/

44. PHENOPSIS DB http://bioweb.supagro.inra.fr/phenopsis/Accueil.php?lang=En

45. Phenomic Data Management Phenomic data management involves three critical components Algorithm and Program Phenotypic Information Sensory data Model Development Genotype and Phenotype Interactions Understand Management Databases Resource Development and Sharing Networking Granier C and Vile D (2014) Curr Opin Plant Biol 18 : 96-102

46. Inter(national) Plant Phenotyping facilities and networks LeasyScan Platform at ICRISAT, Hyderabad – Dr. Vincent Vadez http://www.icrisat.org/research-facilities/ INDIA

47. Indian Plant Phenomics Facilities IIHR, Bengaluru http:// www.nicraicar.in/nicrarevised/images/Home/Inauguration2.jpg CRIDA, Hyderabad http://www.iihr.ernet.in/system/files/Inauguration%20of%20Plant%20Phenomics%20National%20Facility%20at%20ICAR_IIHR%20c.jpg NIASM, Baramati http://www.icar.org.in/files/niam-01-25102016.jpg https://www.siasat.com/news/pm-modi-inaugurating-plant-phenomics-centre-iari-1241436/ IARI, New Delhi

48. Australian Plant Phenomics Facility http :// player.slideplayer.com/18/6119592/data/images/img12.jpg http:// player.slideplayer.com/18/6119592/data/images/img11.jpg AUSTRALIA

49. PlantScan Phenotower TrayScan Cropatron Plant Phenomics Teachers Resource APPF 2010

50. http://seccombe2010.anat.org.au/files/2010/10/IMG_4638.jpg Blimp

51. LEPSE ( Ecophysiology Laboratory of Plants Under Environmental Stress ), Montpellier https://www6.montpellier.inra.fr/lepse_eng/ FRANCE

52. Heliaphen , an outdoors high-throughput automated phenotyping https://www6.toulouse.inra.fr/lipm_eng/Platforms-and-Facilities/Plant-production-and-experimentation-platform/Equipment-Facilities

53. Jülich Plant Phenotyping Center, Forschungszentrum Jülich , Germany GROWSCREEN Rhizo GROWSCREEN Page http:// www.fzjuelich.de/ibg/ibg2/EN/Research/ResearchGroups/JPPC/JPPC_node.html GERMANY

54. Field-Prophet http:// www.fzjuelich.de/ibg/ibg2/EN/Research/ResearchGroups/JPPC/technologies/FieldProphet/FieldProphet_node.html

55. The Nordic Plant Phenotyping Network (NPPN) The European Plant Phenotyping Network (EPPN) The German Plant Phenotyping Network (DPPN) The UK Plant Phenomics Network (UK-PPN) The International Plant Phenotyping Network (IPPN) Plant Phenotyping Networks

56. International Plant Phenotyping Network https://www.plant-phenotyping.org/

57. Case Study-1 Posted July 9, 2017

58. Dr. Lee H ickey , University of Queensland Wheat, Barley & Chickpea (~6gen/ yr ) Mustard (4 gen/ yr ) http://www.bojanglesmuseum.com/4204/nasa-logo-image-14-08-2017/ http ://hickeylab.com/our-projects/speed-breeding/

59. Requirements for speed breeding Watson A et al (2017) bioRxiv p . 161182 doi :  https://doi.org/10.1101/161182

60. Conventional vs Speed Breeding Watson A et al (2017) bioRxiv p . 161182 doi :  https://doi.org/10.1101/161182 video

61. Ear and seed morphology of Triticum aestivum cv. Chinese Spring Speed Breeding Control Watson A et al (2017) bioRxiv p . 161182 doi :  https://doi.org/10.1101/161182

62. Wheat crossing under Speed breeding conditions Efficiency rates for wheat crosses under speed breeding condition Watson A et al (2017) bioRxiv p . 161182 doi :  https://doi.org/10.1101/161182

63. Phenotyping plants under speed breeding conditions Phenotyping under Speed breeding conditions Watson A et al (2017) bioRxiv p . 161182 doi :  https://doi.org/10.1101/161182

64. Applications of speed breeding Speed breeding can greatly accelerate the crop improvement process Can be integrated with other advanced techniques like genomic selection, genome editing, high-throughput genotyping, etc Speed breeding protocols are also being tested by various researchers in other crops like Groundnut and Grain Amaranth to name a few

65. Experimental outline F 7 bulked RILs derived from IR64 (mega variety) X Aswina (high biomass landrace) cross RILs were planted in three cohorts with stagerred planting dates Plot size adjusted for tractor movement (housing HTP platform) 1516 RILs were genotyped by GBS P henotyped manually and by tractor mounted high-throughput platform

66. Tractor-based HTP platform Tanger P et al (2017) Sci Rep 7 :42839 doi:10.1038/srep42839

67. Manual and HTP data collection Summary of HTP data collection HTP Traits : Plant height, NDVI, NDRE, Chl a and Canopy temperature depression Manual data collection at 80 DAS and above – Days to heading, Plant height, Biomass, Grain yield (cohort 3)and Harvest index ( cohort3) Tanger P et al (2017) Sci Rep 7 :42839 doi:10.1038/srep42839

68. The NDVI effect size of QTL [email protected] (Chromosome#@ cM ) Tanger P et al (2017) Sci Rep 7 :42839 doi:10.1038/srep42839

69. Manually-measured traits are genetically correlated with HTP traits across QTL Tanger P et al (2017) Sci Rep 7 :42839 doi:10.1038/srep42839

70. Significant findings of Tanger et al (2017) D etecting QTL with HTP phenotyping is accurate and effective Genomic regions controlling yield and yield components can be identified nondestructively and in a fraction of the time F ield based HTP allows efficient screening of large populations HTP can offer rapid, early prediction of phenotypes leading to better selection of lines

71. Conclusions http:// www.visionsystems.com/content/dam/VSD/onlinearticles/2013/02/vsdnews02182013robot.jpg http:// www.enterrasolutions.com/media/Precision-agriculture-clear-02.png http://www.lorenzlab.net/uploads/1/4/5/7/14579560/8443866_orig.jpg http:// www.travelerfood.com/blog/wp-content/uploads/2015/05/IndianRailways-is-the-9th-largest-employer-of people-in-the-world.jpg http://media.istockphoto.com/vectors/science-concept-collaboration-of-professionals-vector-id465361582 https:// callminer.com/wpcontent/uploads/2015/07/contact-center-efficiency.jpg

72. Thank You…