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Trait phenotyping: About asking the right questions to harness phenomics' progress

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Presentation on Trait phenotyping: About asking the right questions to harness phenomics' progress.
Phenodays 2013 - 17 Oct 2013

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Trait phenotyping: About asking the right questions to harness phenomics' progress

  1. 1. Trait phenotyping: About asking the right questions to harness phenomics’ progress Vincent Vadez – Jana Kholova ICRISAT Phenodays 2013 – 16-18th October 2013
  2. 2. Today’s presentation Basic considerations on trait phenotyping Root / Water extraction Leaf area development Leaf conductance Growth response to soil drying
  3. 3. Grain Yield Grain Number Grain Size & N  Biomass RADN TE T RUE Rint vpd kl LAISLNRoots k  TN LNo A >A APSIM Generic Crop Template, from Graeme Hammer Yield and its determinants Yield is not a trait Phenotyping should focus on the building blocks
  4. 4. Accurate Non accurate Precise Not precise Precision / Accuracy of phenotyping Is my phenotype the right one? Are measurements Good enough?
  5. 5. What is a “drought tolerant” plant? A plant with: • enough water to fill up grains • no more water after grain filling Hypotheses: • Tap water? • Save/manage water? Focus on traits affecting plant water budget
  6. 6. Basic considerations on trait phenotyping Root / Water extraction Leaf area development Leaf conductance Growth response to soil drying
  7. 7. Lysimetric facility at ICRISAT Advantages: • Gravimetric • Long term (3 Wks-maturity) • High throughput (5000 PVCs)
  8. 8. Root length density and water extraction Drought root length density (cm cm-3) 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 Droughtwaterextraction(kgplant-1) 5.5 6.0 6.5 7.0 7.5 8.0 8.5 BRB 191 PAN 127 SUG 131 VAX 1 BAT 477 DOR 364 CAL 143 VAX 3 RCW SEA 5 SEA 15 SER 16 SEQ 1003 SEQ 11CAL 96 SAB 259 RAA 21 ICA Quimbaya SER 8 Mean: 0.56 LSD0.05: 0.13 SEC 16 Mean: 6.84 LSD0.05: 1.53 r = 0.08 No relation between water extraction (WS) and root length / RLD Beans Chickpea
  9. 9. Post-rainy season Rainy season 0 5 10 15 0 1000 2000 3000 4000 5000 6000 7000 Podyield(gplant-1) Total water extracted (g plant-1) 0 2 4 6 8 10 0 1000 2000 3000 4000 5000 6000 7000Podyield(gkg-1) Total water extracted (g plant-1) No relationship between total water extracted and grain yield 0 2 4 6 8 10 12 14 0 1000 2000 3000 4000 5000 6000 7000 Podyield(gplant-1) Total water extracted (g plant-1) Cowpea Peanut 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 0 1000 2000 3000 4000 5000 6000 7000 Podyield(gplant-1) Total water extracted (g plant-1) Bean Peanut Rainy seasonRainy season Pod yield and water extraction
  10. 10. Water extraction pattern (WS) in 12 tolerant / 8 sensitive chickpea Zaman-Allah, Jenkinson, Vadez 2011 JXB 0 1 2 3 4 5 6 7 8 9 10 21 28 35 42 49 56 63 70 77 84 91 98 CumulatedWaterUsed (kgpl-1) Days after sowing Flowering Sensitive Tolerant Tolerant: less WU at vegetative stage, more for reproduction & grain filling
  11. 11. Zaman-Allah, Jenkinson, Vadez 2011 JXB 0 1 2 3 4 5 6 7 8 9 10 21 28 35 42 49 56 63 70 77 84 91 98 Waterused(kgpl-1) Days after sowing Sensitive Tolerant Relationship between grain yield and water use Low early vigor Low leaf Gs Tolerant: less WU at vegetative stage, more for reproduction & grain filling
  12. 12. 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 0 1 2 3 4 WU(kgplant-1week-1) Weeks after panicle emergence ICMH01029 ICMH01040 ICMH01046 PRLT2/89-33 Vadez et al 2013 – Plant Soil H77/833-2 ICMH02042 Terminal drought sensitive Terminal drought tolerant Tolerant: less WU at vegetative stage, more for reproduction & grain filling Water extraction pattern (WS) in pearl millet Flowering
  13. 13. R² = 0.7108 0 4 8 12 16 20 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 Early stress WU in week 3 after panicle emergence GrainYield(gplant-1) Tolerant: EUW = 45 kg grain mm-1 Relationship between grain yield and water use
  14. 14. What platform for phenotyping? • Outdoors / yield-based • Water extraction at key time - Automation • Possible IR surrogates • Staygreen
  15. 15. Basic considerations on trait phenotyping Root / Water extraction Leaf area development Leaf conductance Growth response to soil drying
  16. 16. Leafarea Thermal time A – Fast early LA B – Slow early LA C – Fast early LA / small max LA D – Slow early LA / small max LA Leaf area development dynamics Speed of development / size of canopy = water
  17. 17. Arrows indicates Re-watering Profile of water use from flowering to maturity In peanut Sensitive Tolerant Tolerant lines develop a smaller canopy under WW conditions Ratnakumar and Vadez 2011
  18. 18. Field trial 0 5 10 15 20 25 0 1000 2000 3000 4000 5000 6000 A = 2,91 Fleur 11 WW condition R² = 0,999 Nodes number Leafarea(cm²) Field trial 0 5 10 15 20 25 0 1000 2000 3000 4000 5000 6000 A = 2,63 ICG 1834 WW condition R²= 0.91 Nodes number Leafarea(cm²) Peanut Coefficients relating leaf area to node number Need a HT method to measure the dynamics of leaf area development
  19. 19. Zaman-Allah, Jenkinson, Vadez 2011 JXB 0 1 2 3 4 5 6 7 8 9 10 21 28 35 42 49 56 63 70 77 84 91 98 Waterused(kgpl-1) Days after sowing Sensitive Tolerant Relationship between grain yield and water use Low early vigor
  20. 20. y = 23.302e0.2562x R² = 0.9367 0 2000 4000 6000 8000 10000 12000 0 5 10 15 20 25 Leafarea(cm2) Node number on main stem y = 11.995e0.31x R² = 0.9607 0 2000 4000 6000 8000 10000 12000 0 5 10 15 20 25 Node number on main stem Coefficients relating leaf area to node number Chickpea Need for a leaf count along with leaf area
  21. 21. R² = 0.7255 0 5 10 15 20 25 30 1500 1700 1900 2100 2300 2500 2700 2900 3100 3300 Grainyieldunder Waterstress Leaf area at anthesis Relation between LA and grain yield in postrainy sorghum Higher grain yield is related to lower anthesis leaf area
  22. 22. Variation in leaf area Variation affected by water stress WW&WS- LA development 0 500 1000 1500 2000 2500 3000 18-Nov 23-Nov 28-Nov 3-Dec 8-Dec 13-Dec 18-Dec 23-Dec LA(cm2) 6008 WW 6016 WW 6026 WW 7001 WW S35 WW 6008 WS 6016 WS 6026 WS 7001 WS S35 WS Progressing drought Need to account for: - soil moisture effect - VPD effects Leaf area development response to drought WW WS
  23. 23. Canopy developmental dynamics TPLAvarying TPLA_prod_coef 0 5 10 15 20 25 0 200 400 600 800 TTemerg_to_flag TPLA -0.01 -0.018 -0.026 TPLA_inflection_ratio = 0.66 TPLAmax = 20 0.01 TPLA varying TPLA_inflection_ratio 0 5 10 15 20 25 0 200 400 600 800 TTemerg_to_flag TPLA 0.66 0.5 0.33 TPLAmax = 20 TPLA_prod_coef - 0.018 0.33 0.66 LA development depends on: •TPLA production coefficient and •TPLA inflection ratio
  24. 24. 0 500 1000 1500 2000 2500 3000 02.4823.914 5.266.5847.9969.44410.7220.36275.504141.84212.9281.47346.74413.21465.36521.08566.23612.08654.97694.29731.48761.5782.41807.44858.98920.38977.521040.4 thermal time kgha-1 0 0.2 0.4 0.6 0.8 1 1.2 1.4 m2m-2 stover TR high stover TR low grain TR high grain TR low LAITR high LAITR low SD TR high SD TR low Simulation:severe terminal drought Delayed senescen ce Delayed water exhaustion LAI S/D ratio biomass water conservation during vegetative growth and its utilization for better grain filling = stay-green kgha-1 Thermal time YIELD flowering ~830 0dayStaygreen phenotype is a consequence of smaller/delayed leaf development
  25. 25. What platform for phenotyping? • 3-D imaging of Leaf Area • Measurements at early stages • Soil moisture effects • VPD effects (need HT measurements)
  26. 26. Basic considerations on trait phenotyping Root / Water extraction Leaf area development Leaf conductance Growth response to soil drying
  27. 27. Vapor Pressure Deficit (VPD, in kPa) Transpirationrate(gcm-2h-1) 0.0 2.0 4.0 0.0 1.0 A – Insensitive to VPD – High rate at low VPD B – Sensitive to VPD – High rate at low VPD C – Sensitive to VPD – Low rate at low VPD D – Insensitive to VPD – Low rate at low/high VPD Main types of Tr response to VPD Water use difference Leaf conductance differences = water Vadez et al 2013 – FPB in press
  28. 28. Terminal drought sensitive Terminal drought tolerant 0.005 0.01 0.015 0.02 0.025 0.03 0.035 0.04 0.045 0.50 1.00 1.50 2.00 2.50 3.00 3.50 VPD (kPa) H77/2 833-2 PRLT-2/89-33 Transpiration(gcm-2h-1) From Kholova et al 2010b 2 mechanisms of water saving: •Low Tr at low VPD •Further restriction of Tr at high VPD Transpiration response to high VPD – Pearl millet
  29. 29. 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 0 1 2 3 4 WU(kgplant-1week-1) Weeks after panicle emergence ICMH01029 ICMH01040 ICMH01046 PRLT2/89-33 Vadez et al 2013 – Plant Soil H77/833-2 ICMH02042 Terminal drought sensitive Terminal drought tolerant Tolerant: less WU at vegetative stage, more for reproduction & grain filling Water extraction pattern (WS) in pearl millet Flowering Water saving from lower conductance
  30. 30. 4 replications RH & T hourly recording Weighing: 7-11am = low VPD 11am-15pm = high VPD 8” pots re-saturated every day soil evaporation minimized with plastic beads Mapping of water saving traits
  31. 31. Transpiration response to high VPD - Peanut
  32. 32. -1 0 +33 15-30% yield decrease, especially at high latitudes (12-15ºN) % yield increase with VPD response trait - Peanut
  33. 33. Mouride IfVPD<2.09,TR=0.0083(VPD)–0.002 IfVPD≥ 2.09,TR=0.0013(VPD)+0.015 R²=0.97 B UC-CB46 TR=0.0119(VPD)-0.0016 R²=0.97 D Transpiration response to VPD - cowpea Tolerant lines have a breakpoint (water saving) Tolerant Sensitive Belko et al – 2012 (Plant Biology)
  34. 34. R² = 0.64 -40 -20 0 20 40 60 0.000 0.010 0.020 0.030 0.040 0.050 0.060 Residualtranspiration Transpiration rate under high VPD What drives transpiration in that population?? Leaf area (69%) Conductance at high VPD (64% of residual) Phenotype both these traits (LA – Transpiration response to VPD) R² = 0.69 0 50 100 150 200 250 0 200 400 600 800 1000 1200 Totaltranspiration (gplant-1) Leaf area (cm2 plant-1)
  35. 35. QTLs from ICI Mapping – Drought tolerance traits TraitName Chromo some Position (cM) Flanking markers LOD PVE(%) Additive effect Positive allele Plt DW 2 4 1_0113 - 1_0021 3.1 15.5 0.3 CB46 SLA 2 31 1_1139 - 1_1061 3.6 14.4 -11.5 IT93K-503-1 LA 2 85 1_0834 - 1_0297 4.0 18.5 57.0 CB46 Leaf DW 2 85 1_0834 - 1_0297 2.8 13.4 0.2 CB46 Plant transp Total 6h 2 85 1_0834 - 1_0297 2.9 13.1 8.9 CB46 Conductance High VPD 5 19 1_0806 - 1_0557 3.2 16.3 0.0 IT93K-503-1 Conductance Low VPD 5 20 1_0806 - 1_0557 2.8 13.3 0.0 IT93K-503-1 Conductance Low VPD 5 23 1_0806 - 1_0557 3.3 14.0 0.0 IT93K-503-1 Conductance Low VPD 7 13 1_0279 - 1_1482 3.6 15.0 0.0 IT93K-503-1 SLA 9 25 1_0051 - 1_0048 4.9 19.7 13.5 CB46 Conductance high VPD 9 52 1_0425 - 1_1337 2.6 11.5 0.0 IT93K-503-1
  36. 36. What platform for phenotyping? • 3-D imaging of Leaf Area • Leaf area + Transpiration together • VPD effects
  37. 37. Basic considerations on trait phenotyping Root / Water extraction Leaf area development Leaf conductance Growth response to soil drying
  38. 38. Fraction of Transpirable Soil Water (FTSW) Norrmalizedtranspiration 1.0 0.5 0.00.25 0.0 1.0 Growth response to water stress 0.75
  39. 39. Fraction of Transpirable Soil Water (FTSW) Norrmalizedtranspiration 1.0 0.5 0.00.25 A – Standard genotype B – Early stomata closure C – Late stomata closure 0.0 1.0 Growth response to water stress Early growth decline = water saving 0.75
  40. 40. Fraction of Transpirable Soil Water (FTSW) Norrmalizedtranspiration 1.0 0.5 0.00.25 A – Standard genotype B – Early stomata closure C – Late stomata closure 0.0 1.0 B’ – Early stomata closure + stress relief C’ – Late stomata closure + stress relief Irrigation or rain Growth response to water stress Water saving, but… 0.75
  41. 41. 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate ---- ---- Bambey 21:FTSW = 0.63 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate Mouride:FTSW = 0.44 (A) Glasshouse 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate ---- ---- IT82E-18:FTSW = 0.62 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate IT84S-2049:FTSW = 0.47 (B) Glasshouse 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate ---- ---- Bambey 21:FTSW = 0.69 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate Mouride:FTSW = 0.48 (C) Outdoors 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate ---- ---- IT82E-18:FTSW = 0.71 0.00.20.40.60.81.0 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 Fraction of transpirable soil water Normalizedtranspirationrate IT84S-2049:FTSW = 0.49 (D) Outdoors Soil moisture thresholds for transpiration decline - cowpea
  42. 42. (A) (B) Soil moisture thresholds for transpiration decline - chickpea
  43. 43. What platform for phenotyping? • Plant transpiration • Automatic re-watering to set weight
  44. 44. In summary New technologies offer great opportunities Platform development driven by research questions Traits: building block or emerging consequence?? Link of traits to yield Trait response to environmental cues
  45. 45. Thank you Collaborators: F. Chaumont (Univ. Louvain) G. Hammer / A. Borrell / G McLean / E van Oosterom (Univ. Queensland) B Sine / N Belko / Ndiaga Cisse (CERAAS) C Messina (Pioneer) Donors: B&MG Foundation GCP ACIAR DFID ICRISAT Technicians / Data analyst: Srikanth Malayee Rekha Badham M Anjaiah N Pentaiah Students: M Tharanya S Sakthi T Rajini N Belko Colleagues: KK Sharma / T Shah / F Hamidou HD Upadhyaya / R Srivastava / Bhasker Raj SP Deshpande / PM Gaur

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