GCP 2011General ResearchMeeting21-25 Sep 2011L KrishnamurthyICRISATChickpeas - Phenotyping for drought traits
• Trait’s relevance for phenotyping• Framework for trait choice: Analyticalmodel explaining yield• Phenotyping experience ...
Drought type - strategies (intensity/timing/duration)Trait that matters & linked to yieldLink trait-environmentConstitutiv...
• Phenotyping for root systemStructural and FunctionalJ. Kashiwagi, L. Krishnamurthy, H.D. Upadhyaya,P.M. Gaur, R.K. Varsh...
•Establishing the contribution of root traits to DRT yield infield,•Assessment of root variation in field using an RILs•Es...
Variation in rooting depthRootingdepth(cm)859095100105110115120125130Mini-core germplasm accessions (n=211) plus 5 popular...
Variation in root length densityMini-core germplasm accessions (n=211) plus 5 popular cultivars grown in cylinder systems ...
ICCM0249TAA170GA24STMS11CID traitsRoot traitsICCM0249TAA170GA24STMS11Root + CID + Yield traitsHot spot for QTL –LG 5(ICC 4...
Root function – Transpiration measurementsDynamic obs.Root functioni.e. actual transpiration
Root phenotypingAre there simple solutions?
Root traits – How useful is the seedling expression?Contrasting selections of 10 day-old chickpea seedlings from therefere...
- for a high throughput assessment ofcanopy temperature or root functionL. Krishnamurthy, Z.A. Mainassara,J. Kashiwagi, R....
IR Photograph IR Photo devoid of soil radiationAdvantage overIR Thermometer:Observer biasgets minimizedCanopy temperature•...
202224262830323436ICC 1882 ICCV10 ICC 867 Annigeri ICC14799ICC 283 ICC 8261 ICC14778ICC 4958 ICC 3325 ICC 3776 ICC 7184Opt...
Variation in canopy temperature across 60 drought tolerantand 24 sensitive genotypes at 75 DAS, 2009-10.272829303132333435...
Well-watered conditions Water stressLeaf conductance(g h-1cm-2)CanopyTºCShoot DW LeafexpansionTotalTrFTSWThresholdShoot DW...
Phenotyping for TE (through Δ13C)
How does TE contributeto drought tolerance?Yield = Shoot biomass x Harvest indexTranspiration Transpiration Efficiency (TE...
… and the optimally irrigated section of the DT field evaluationof the reference collection of chickpea germplasm
Means (BLUPs) and range of various traits observed both under drought stressedand optimally irrigated environments of the ...
10 leavesAt 63 DAS, Recently formedFully expandedPrimary branch-bornfrom 10 different plantsDried at 60°C for three daysC ...
The relationship between per day productivity (grain yield kg ha-1 day-1) orWUE with carbon isotope discrimination - 2008-...
Other traits that get affected by Δ13CCorrelations of carbon discrimination (Δ13C) with other drought-related traitsobserv...
The relationship between leaf Δ13C under drought stress with thatunder optimally irrigated in the 280 accessions of the ch...
Phenotyping for Harvest index
Partitioning Coefficient or Rate of Partitioningy = 25.1x + 572.0r2= 0.72050010001500200025000 10 20 30 40 50 60Harvest in...
What happens to the growth duration under ter. drt?35.1 54.035.8 76.50 20 40 60 80 100 120Optimally irrigatedDrought stres...
The value of harvest index under terminal droughtDirect and indirect contributions of HI to Seed yield in the referencecol...
The value of harvest index under terminal droughtDirect and indirect contributions of Pods m-2 to Seed yield in thereferen...
Partitioning Coefficient or Rate of Partitioning
The relationship of seed yield with partitioning coefficient across 19(year1)and 40 (year 2) advanced breeding lines grown...
Yield-based approachfor assessingDrought Tolerance
The drought stressed section of the DT field evaluationof the reference collection of chickpea germplasm
Residuals derived using the multiple regression approach.This approach considers grain yield under drought stress (Ys)as a...
Drought tolerance indices and seed yield at maturity of the highly droughttolerant and highly drought sensitive mini core ...
Conclusions• Many-fold phenotypic variation exists in the referencecollection for roots (structure & function), canopytemp...
Thankyou
GRM 2011: Phenotyping chickpeas for drought tolerance
GRM 2011: Phenotyping chickpeas for drought tolerance
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GRM 2011: Phenotyping chickpeas for drought tolerance

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GRM 2011: Phenotyping chickpeas for drought tolerance

  1. 1. GCP 2011General ResearchMeeting21-25 Sep 2011L KrishnamurthyICRISATChickpeas - Phenotyping for drought traits
  2. 2. • Trait’s relevance for phenotyping• Framework for trait choice: Analyticalmodel explaining yield• Phenotyping experience for- Root structure and function (TL1)- Canopy temperature- TE through Δ13C (GCP : SP3 G4008-12)- Rate of partitioning- For drought tolerance indicesChickpeas - Phenotyping for drought traits
  3. 3. Drought type - strategies (intensity/timing/duration)Trait that matters & linked to yieldLink trait-environmentConstitutive vs adaptive traitsNon-stress related factors affecting yielde.g.: Time to flowering & Yield potentialExpl. design – Data qualitySimple, precise, high throughput amenableChoice of traits to phenotype
  4. 4. • Phenotyping for root systemStructural and FunctionalJ. Kashiwagi, L. Krishnamurthy, H.D. Upadhyaya,P.M. Gaur, R.K. Varshney,Z.A. Mainassara, V. Vadez and others
  5. 5. •Establishing the contribution of root traits to DRT yield infield,•Assessment of root variation in field using an RILs•Establishment of acceptable protocols that produce closelyrelated root performance in cylinders•Phenotypic assessment for root related traits in theminicore germplasm, three mapping populations and thereference collection•And identification of robust QTLs are the achievements ofthe past decadeChickpeas - Phenotyping for root traits
  6. 6. Variation in rooting depthRootingdepth(cm)859095100105110115120125130Mini-core germplasm accessions (n=211) plus 5 popular cultivars grown in cylinder systems andsampled at 35-d after sowing.ICC8261ICC4958AnnigeriICC 283ICC1882SEd=12.95
  7. 7. Variation in root length densityMini-core germplasm accessions (n=211) plus 5 popular cultivars grown in cylinder systems andsampled at 35-d after sowing.0.180.200.220.240.260.280.300.32Rootlengthdensity(cmcm-3)ICC8261ICC4958AnnigeriICC283ICC1882SEd=0.022
  8. 8. ICCM0249TAA170GA24STMS11CID traitsRoot traitsICCM0249TAA170GA24STMS11Root + CID + Yield traitsHot spot for QTL –LG 5(ICC 4958 × ICC 1882 map)
  9. 9. Root function – Transpiration measurementsDynamic obs.Root functioni.e. actual transpiration
  10. 10. Root phenotypingAre there simple solutions?
  11. 11. Root traits – How useful is the seedling expression?Contrasting selections of 10 day-old chickpea seedlings from thereference collection - sand culture.
  12. 12. - for a high throughput assessment ofcanopy temperature or root functionL. Krishnamurthy, Z.A. Mainassara,J. Kashiwagi, R. Purushothaman &V.VadezInfrared thermography
  13. 13. IR Photograph IR Photo devoid of soil radiationAdvantage overIR Thermometer:Observer biasgets minimizedCanopy temperature• Simple• Truly high throughput• Yet to be established• Critical stage ofobservation
  14. 14. 202224262830323436ICC 1882 ICCV10 ICC 867 Annigeri ICC14799ICC 283 ICC 8261 ICC14778ICC 4958 ICC 3325 ICC 3776 ICC 7184Optimally irrigatedDrought stressedVariation in canopy temperature across 8 drought tolerantand 4 sensitive genotypes at early-pod fill stage, 2009-10.
  15. 15. Variation in canopy temperature across 60 drought tolerantand 24 sensitive genotypes at 75 DAS, 2009-10.2728293031323334351 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76Germplasm accessionsC.areaxC.temp.(0C)25272931333537391 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76Canopytemp.(0C)0.80.911 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76CanopyproportionEvap. 5.1mmMax T. 30.0 0CMin T. 9.0 0C
  16. 16. Well-watered conditions Water stressLeaf conductance(g h-1cm-2)CanopyTºCShoot DW LeafexpansionTotalTrFTSWThresholdShoot DW42 DASOutdoor42 DASGC*42 DAS 42DAS56DAS42-56DAS56 DAS 56 DASICC867 Low Low Hot Low Low Low High LowICC3325 Low Low Hot Low Low High LowICC3776 High Cool High Low HighICC4814 High High Cool Low High Low HighICC7184 Cool High High High LowICC8058 High High Cool High High High High Low HighICC14778 Low Low Low Low High LowICC14799 Low Low Hot Low Low Low Low High Low1
  17. 17. Phenotyping for TE (through Δ13C)
  18. 18. How does TE contributeto drought tolerance?Yield = Shoot biomass x Harvest indexTranspiration Transpiration Efficiency (TE)=13CxLeaf biomass + Stem biomassLAxLeaf biomass/Leaf area ratio (inverse of specific leaf area: SLA)SPADIncreasing SLA=reducing the water loss via leaf area reduction + maintain photosynthesis vialeaf thickness increase
  19. 19. … and the optimally irrigated section of the DT field evaluationof the reference collection of chickpea germplasm
  20. 20. Means (BLUPs) and range of various traits observed both under drought stressedand optimally irrigated environments of the 280 accessions of the referencecollection of chickpea germplasm during 2008-09 postrainy season in a Vertisol. (Allthe traits showed significantly different many-fold variation)___________________________________________________________________Drought stressed Optimally irrigated__________________ ___________________Characteristics Mean Range Mean Range____________________________________________________________________Days to 50% flowering 51 39-71 54 40-69Days to maturity 98 83-120* 115 109-126*Shoot biomass (kg ha-1) 3444 2259-4726 5263 3602-6977Seed yield (kg ha-1) 1557 510-2250 2057 1004-3029Harvest index 46 11-61 39.4 17.3-52.8Pod number m-21358 512-2332 1965 802-4553Seed number m-21614 504-3131 2516 831-4553Seeds pod-11.2 1.0-1.5 1.3 1.0-1.9100 seed weight (g) 16.3 8.8-36.2 15.1 7.2-44.6Shoot biomass (kg ha-1day-1) 35.1 20.7-46.9 45.7 30.6-58.9Seed yield (kg ha-1day-1) 32.2 8.5-48.2 39.9 17.7-50.1___________________________________________________________________
  21. 21. 10 leavesAt 63 DAS, Recently formedFully expandedPrimary branch-bornfrom 10 different plantsDried at 60°C for three daysC isotope measurements at JIRCAS
  22. 22. The relationship between per day productivity (grain yield kg ha-1 day-1) orWUE with carbon isotope discrimination - 2008-09.y = -3.6x - 62.9r2= 0.11***0102030405060-28.5 -28.0 -27.5 -27.0 -26.5 -26.0 -25.5 -25.0Δ13CGrainyield(kghaday-1)A relation significant only under drought stress)
  23. 23. Other traits that get affected by Δ13CCorrelations of carbon discrimination (Δ13C) with other drought-related traitsobserved with the 280 accessions of the reference collection of the chickpeagermplasm in 2008-09.____________________________________________________________________Δ13C-----------------------------------------------Characteristics Drought stressed Optimally irrigated____________________________________________________________________Days to 50% flowering -0.019 0.103Days to maturity 0.102 0.147Shoot biomass (kg ha-1) 0.153 0.160Seed yield (kg ha-1) -0.193*-0.232*Harvest index -0.334***-0.406***Pod number m-2-0.383***-0.273**Seed number m-2-0.378***-0.264**Seeds pod-1-0.182 -0.043100 seed weight (g) 0.321***0.101Shoot biomass (kg ha-1day-1) 0.091 0.131Seed yield (kg ha-1day-1) -0.263**-0.207*___________________________________________________________________
  24. 24. The relationship between leaf Δ13C under drought stress with thatunder optimally irrigated in the 280 accessions of the chickpeareference collection in 2008-09.y = 0.47x - 15.2r2= 0.36***-29.5-29.0-28.5-28.0-27.5-27.0-26.5-28.5 -28.0 -27.5 -27.0 -26.5 -26.0 -25.5 -25.0Δ13C - Drought stressedΔ13C-Optimallyirrigated
  25. 25. Phenotyping for Harvest index
  26. 26. Partitioning Coefficient or Rate of Partitioningy = 25.1x + 572.0r2= 0.72050010001500200025000 10 20 30 40 50 60Harvest index (%)Grainyieldunderdroughtstress(kgha-1)Relation ship of HI with drought yield in CP refernce collection, 2009-10___________________________________________________________________Shoot Seed HarvestBiomass yield indexNo Accession (kg ha-1) (kg ha-1) (%)__________________________________1 ICC 12324 4785 1496 302 ICC 8151 4923 1516 293 ICC 11879 4754 1517 304 ICC 7150 4804 1517 305 ICC 5878 3311 1530 526 ICC 12866 3237 1538 537 ICC 5879 3273 1572 548 ICC 13892 3413 1576 51______________________________________________________________________E.g. Reference collectionaccessions with large HI variationbut not reflecting in yield.Harvest index in reference collectionis well associated with yield.
  27. 27. What happens to the growth duration under ter. drt?35.1 54.035.8 76.50 20 40 60 80 100 120Optimally irrigatedDrought stressed0 20 40 60 80 100 120Optimally irrigatedDrought stressedVegetative ReproductiveVegetative ReproductiveICC 16374Mean in reference set
  28. 28. The value of harvest index under terminal droughtDirect and indirect contributions of HI to Seed yield in the referencecollection of chickpea germplasm in the drought-stressed andoptimally irrigated environments in 2008-09 & 2009-10 seasons(Association and suggestions of HDU et al. acknowledged)-0.400-0.2000.0000.2000.4000.6000.8001.0001.2001.4002008-09-IR 2008-09-NI 2009-10-IR 2009-10-NIYear x soil water environmentPathcoefficientsDelta 13CDays to 50% flrDays to MaturityHIShoot DM (kg ha-1)Pod No m-2100 Seed weight gContribution of HI to yield
  29. 29. The value of harvest index under terminal droughtDirect and indirect contributions of Pods m-2 to Seed yield in thereference collection of chickpea germplasm in the drought-stressedand optimally irrigated environments in 2008-09 & 2009-10 seasons(Association and suggestions of HDU et al. acknowledged)-0.400-0.2000.0000.2000.4000.6000.8001.0002008-09-IR 2008-09-NI 2009-10-IR 2009-10-NIYear x soil water environmentPathcoefficientsDelta 13CDays to 50% flrDays to MaturityHIShoot DM (kg ha-1)Pod No m-2100 Seed weight gContribution of Pod No m-2to yield
  30. 30. Partitioning Coefficient or Rate of Partitioning
  31. 31. The relationship of seed yield with partitioning coefficient across 19(year1)and 40 (year 2) advanced breeding lines grown under droughtstressed and optimally irrigated environments (Krishnamurthy et al. 1999)
  32. 32. Yield-based approachfor assessingDrought Tolerance
  33. 33. The drought stressed section of the DT field evaluationof the reference collection of chickpea germplasm
  34. 34. Residuals derived using the multiple regression approach.This approach considers grain yield under drought stress (Ys)as a function of yield potential (Yp), time to 50% flowering (F),and a drought tolerance index (DTI) such that the yield of agenotype can be expressed as follows:Ysi = a + bYp + cFi + DTIi + E,where E is random error with zero mean and variance σ.Standard residuals (= DTI) were calculated as the differencebetween the actual and estimated yields under stress uponthe standard error of the estimated yield (σ).For this multiple regression, 50% flowering (Fi) under stress for every individualplot and for the Yield potential (Yp) arithmetic mean across the three replicationswere considered. (Bidinger et al., 1987; Saxena et al., 1987; Saxena, 2003; Vadez et al.,2007; Krishnamurthy et al. 2010; 2011)Yield-based approach
  35. 35. Drought tolerance indices and seed yield at maturity of the highly droughttolerant and highly drought sensitive mini core chickpea germplasmaccessions.___________________________________________________________________________________________________S.No Accession Drought Seed Drought Seed Drought Seedtol. Index yield (kg ha-1) tol. Index yield (kg ha-1) tol. Index yield (kg ha-1)2002-03 2002-03 2005-06 2005-06 2006-07 2006-07___________________________________________________________________________________________________Highly drought tolerant1 ICC 867 0.71 2472 0.28 924 1.26 16202 ICC 1923 0.52 1541 0.57 1059 1.10 17753 ICC 9586 0.90 1900 0.31 784 1.18 13284 ICC 12947 1.36 2368 0.50 998 0.61 13635 ICC 14778 1.11 2570 0.47 1035 1.24 1636Mean 0.92 2170 0.43 960 1.08 1544Highly drought sensitive1 ICC 1052 -0.70 1196 -0.09 642 -0.76 9102 ICC 2242 -1.10 261 -0.25 226 -1.38 3763 ICC 2720 -0.86 797 -0.35 213 -1.44 4174 ICC 2990 -0.62 945 -0.25 431 -0.78 9135 ICC 3776 -1.35 813 -0.03 719 -0.63 10276 ICC 4814 -0.79 943 -0.18 726 -0.64 8317 ICC 6263 -1.24 1151 -0.04 866 -0.95 11758 ICC 6306 -0.41 220 -0.10 229 -1.02 4099 ICC 7184 -0.87 827 -0.48 457 -1.48 76210 ICC 7819 -0.42 668 -0.02 458 -1.06 104611 ICC 8058 -1.18 973 -0.31 600 -0.82 105712 ICC 11764 -0.90 1013 -0.26 429 -0.34 96813 ICC 11879 -0.93 986 -0.12 702 -0.68 113814 ICC 12537 -0.58 1873 -0.23 683 -0.85 123015 ICC 12928 -0.82 1140 -0.40 512 -0.68 113016 ICC 13124 -1.25 2252 -0.14 1035 -0.55 175317 ICC 13441 -0.78 344 -0.02 424 -1.15 59818 ICC 14669 -0.89 1981 -0.31 788 -0.54 170919 ICC 16374 -1.66 1306 -0.42 632 -0.59 113120 ICCV 2 -1.26 2102 -0.23 729 -0.60 1403Mean -0.93 1090 -0.21 575 -0.85 999___________________________________________________________________________________________________
  36. 36. Conclusions• Many-fold phenotypic variation exists in the referencecollection for roots (structure & function), canopytemperature, Δ13C, rate of partitioning, drought yield& DTIs.• QTLs associated with most drought tolerance traits(like roots and Δ13C ) appear at a hotspot.• The rate of partitioning is known to confer yieldadvantages under terminal drought; however the GxEinteraction & marker association is yet to beascertained
  37. 37. Thankyou
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