Root traits behind major-effect drought-yield QTLs in rice

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1 Colorado State Univ. Drought Symposium, 2012 Root traits behind major-effect drought-yield QTLs in rice Amelia Henry

2 Rice root types Root hairs nodal Root anatomy lateral seminal IR64 Well-watered 12 days after sowing

3 Rice has several different classes of roots, each with distinct diameters

4 Root/drought research at IRRI: ongoing for the last 40+ years Emphasis: deep and thick roots for drought resistance IRRI, 1978 IRRI, 1983 B. Courtois, 1995

5 Drought research at IRRI 1970s 1980s Drought screening of thousands of genotypes in field and greenhouse 1990s Drought breeding strategy: selection for traits ( deep and thick roots ) Identification of QTLs for root traits 2000s Drought breeding strategy: direct selection for yield under drought Identification of QTLs for yield under drought Photo courtesy of B. Courtois

6 Major drought grain yield QTLs in the background of high yielding popular varieties Recipient QTL (s) Chr. Region Add. (%) Donor Vandana qdty RM28048-RM Way Rarem IR64 qdty 1.1 qdty 1.2 qdty 2.2 qdty 4.1 qdty 9.1 qdty RM RM12091 RM212- RM315 RM236- RM279 RM335- RM518 RM566- RM24350 RM258- RM N22 N22 Aday sel Aday sel Aday sel Aday sel Swarna qdty 1.1 qdty 2.1 qdty RM RM12146 RM521- RM6374 RM520- RM N22 Apo Apo Sabitri qdty 3.2 qdty RM569-RM517 RM RM IR IR MTU1010 qdty RM RM N22 TDK 1 qdty qdty RM520-RM16030 RM IR IR

7 DTY 1.1 : multiple donors - multiple backgrounds Dhagaddeshi x Swarna Dhagaddeshi x IR64 Additive effects in five populations for grain yield under drought N22 Swarna 30.20% N22 IR % N22 MTU % Dhagaddeshi Swarna 24.80% Dhagaddeshi IR % Vikram et al. 2011, BMC Genetics 2011

8 Drought Research at IRRI IRRI Climate Unit

9 Rainout shelters and sensor rack for NDVI and IRT S. Klassen

10 IRRI Greenhouse lysimeter facility ~1m-tall PVC cylinders Simultaneous measurements of water uptake and leaf area

11 Root sampling in the field

12 Identification of physiological mechanisms behind drought-yield QTLs Upland rice Lowland rice Planting Drought stressed Vandana x Way Rarem single QTL (qdty 12.1 ) IR64 x Aday Sel NILs 4 QTLs

Sequence for studying physiological mechanisms of drought

Ensure uniformity in stress treatment and characterize the

13 Sequence for studying physiological mechanisms of drought tolerance in QTLs 1. Receive + and QTL lines from breeders that show contrasting yield under drought 2. Ensure uniformity in stress treatment and characterize the drought stress 3. Phenotyping High throughput methods detailed methods If +QTL lines show better water uptake when the soil is dry, we look for root-related mechanisms

14 Major-effect drought yield QTL 12.1 Identifying the underlying mechanisms of improved yield under drought Evidence for a role of QTL 12.1 in water uptake: Bernier et al. (2009) : 7% greater water uptake in +QTL lines under drought in lysimeters Photos courtesy of Tess Sta Cruz

15 No differences in root growth at depth, but qdty 12.1 affected root diameter DS upland Root length density 2010DS upland Average root diameter ** Soil depth (cm) WS upland Root length density IR B (-) IR B (-) IR B (+) IR B (+) Vandana Way Rarem * 2010WS upland Average root diameter IR B (-) IR B (+) Vandana Way Rarem ANOVA p-value QTL 0.05* Soil depth 0.05* QTL X soil depth 0.2ns Root length density (cm cm -3 ) Average root diameter (mm)

16 Distribution of root length within diameter classes Percent of total root length in diameter class A. 2010DS upland cm Root diameter: <0.05 mm mm mm mm mm >1.0 mm IR B IR B * ** * ** none IR B IR B Vandana Way Rarem -QTL +QTL parents

17 QTL 12.1: seedling stage greenhouse study +QTL lines had a larger proportion of fine (lateral) roots than -QTL lines under drought B-B (+QTL) B-B (-QTL) Hypothesis: greater root branching induced by drought stress in +QTL lines improves water uptake from drying soil

18 Detection of fine roots: Comair vs Winrhizo <0.05 mm diameter

19 Canopy temp (C) Rainout shelters: some evidence for a role of QTL 12.1 in water uptake QTL lines had lower canopy temperatures and greater stomatal conductance during severe drought stress in the field 110 -QTL 2010WS ROS Expt 2b QTL QTL days after sow ing 2010DS QTL cm IR B-B IR B-B Vandana Way Rarem Canoy temperature ( o C) Stomatal conductance (mmol m -2 s -1 ) A. 2010DS 59 DAS r 2 = 0.23, p = 0.02* B. 2010WS 70DAS % of initial soil moisture after rewatering QTL das Canoy temperature ( o C) QTL +QTL Vandana Way Rarem r 2 = 0.25, p= Stomatal conductance (mmol m -2 s -1 )

G x E : Effects of soil texture on the performance of qdty12.1 NILs Is greater lateral root growth effective for improved water uptake in different types of soil?

20 G x E : Effects of soil texture on the performance of qdty12.1 NILs Is greater lateral root growth effective for improved water uptake in different types of soil? DD no sand Water uptake (g/day/cm2 leaf) IR B IR B IR90020: B-1 IR90020: B-4 Vandana WayRarem DD sand water uptake (g/day/cm2 leaf) IR B IR B IR90020: B-1 IR90020: B-4 Vandana WayRarem

0 56 58 60 62 64 66 68 70 72 74 78 80 82 84 86 88 90 92 94 96 98 40 45 50 55 60 65 70 Days after sowing Days after sowing Days after sowing ** *** ** * ** Gowda et al.

21 Trials in lowland vs upland soils show different drought responses in terms of water uptake patterns 4.0 A. Trial 1 B. Trial 2 C. Trial 3 OryzaSNP Normalized water uptake rate (kg day -1 / initial kg day -1 ) Azucena Cypress Dular FR13A IR64 LTH *** ** Days after sowing Days after sowing Days after sowing ** *** ** * ** Gowda et al Functional Plant Biology Water uptake rate (g d -1 cm -2 ) B WS *** *** IR86153-B1-B10-B IR86151-B1-205-B IR86153-B1-B11-B IR86151-B1-8-B IR86153-B1-604-B IR86153-B1-B6-B IR64 Dular Swarna RAM x IR64 Kijoji et al. In review Days after sowing Lowland soils: consistent trends in water uptake across the drought period water uptake under drought was correlated with root growth at depth

22 Genotypes adapted to upland soils: more rapid drydown regulation of transpiration DD sand water uptake (g/day/cm2 leaf) IR B IR B IR90020: B-1 IR90020: B-4 Vandana WayRarem Droughttolerant Droughtsusceptible IRRI ICRISAT chickpea Zaman-allah et al., 2011

23 Next: Trials of NILs in a range of soil textures at target drought sites yield root samples Barwale Found. IGKV, Raipur Rajshahi, Bangladesh Hazaribag Raipur Rewa Tripura Hardinath Nepalganj Tarharra Patna Bihar Ag. Univ. Faizabad ICAR, Tripura NDUAT, Faizabad Barwale Foundation JNKVV, Rewa CRURRS Hazaribag DRR Hyderabad

24 Summary: qdty12.1 appears to increase water uptake when the soil is dry through increased lateral root growth under drought Other drought traits/mechanisms may be conferred by qdty 12.1, such as transpiration efficiency B-B (+QTL) B-B (-QTL) IR90020: B-4-B Vandana

25 Aday Sel x IR64 QTL lines

26 Performance of Aday Sel x IR64 QTL lines under drought IR B-B-B IR B-B-B IR64 CRURRS, Hazaribag, India 2011 WS

27 Aday Sel x IR64 NILs +QTL QTL

28 Aday Sel NIL pairs show large differences in canopy temp under severe drought IR64 -QTL QTL QTL QTL Aday Sel

Oryza SNP panel: Canopy temperature was related to root length density 31 Canopy temperature ( C) 30 29 2010DS 15-30 cm r 2 = 0.

29 Oryza SNP panel: Canopy temperature was related to root length density 31 Canopy temperature ( C) DS cm r 2 = 0.40* Azucena Dular IR64 LTH Root length density (cm cm -3 ) Henry, Gowda, Torres, and Serraj, 2011, Field Crops Research

30 Aday Sel NIL pairs did not show large differences in root length density at depth Expt 4s Aday Sel ROS RLD (cm cm -3 ) cm cm IR 64 IR IR IR IR QTL - QTL + QTL - QTL

dry-down from 75% field capacity Lower Lpr in + QTL lines from Aday Sel x IR64

31 Root function for water uptake: hydraulic conductance log Sap flux at 500 kpa (m 3 s -1 ) 1e-9 1e-10 1e-11 well-watered control dry-down from field capacity dry-down from 75% field capacity Lower Lpr in + QTL lines from Aday Sel x IR64 1e-12 IR64 IR (+) IR (-) IR (+) IR (-)

14-1-2-13 (- QTL) Hypothesis: smaller xylem vessel diameters in

32 + QTL lines had smaller root and xylem vessel diameters only near the root tip, and only in the drought treatment (+ QTL) (- QTL) Hypothesis: smaller xylem vessel diameters in +QTL lines result in decreased xylem cavitation under severe stress

Dular and KDML decreased root xylem diameter with increasing drought stress late metaxylem diam. ( m) 42 40 38 36 34 32 30 E.

33 Dular and KDML decreased root xylem diameter with increasing drought stress late metaxylem diam. ( m) E. Exp 2b late metaxylem Dular IR64 KDML 105 WW DD DD-75% well watered drought severe drought A. Henry, A. Cal, T. Batoto, R. Torres, R. Serraj. In Press. Journal of Experimental Botany

shoot) 3.0 2.5 2.0 1.5 1.0 0.5 0.0 3.0 2.5 2.0 1.5 1.0 0.5 C. Bleeding rate, Exp 1a control E.

34 Bleeding rate measurements in the field: Dular and KDML showed consistently lowest bleeding rates compared to droughtsusceptible varieties Bleeding rate (g sap g -1 shoot) Bleeding rate (g sap g -1 shoot) C. Bleeding rate, Exp 1a control E. Bleeding rate, Exp 1a drought Days after sowing Dular IR42 IR64 KDML 105 Moroberekan Swarna

Bleeding rates in IR64x Aday Sel NILs Exp 4 March 14 2012 - stress 0.26 0.24 sap per g shoot 0.22 0.2 0.18 0.16 0.14 0.12 0.

35 Bleeding rates in IR64x Aday Sel NILs Exp 4 March stress sap per g shoot IR64 IR B- B-B IR B- B-B IR B-B- B Exp 4 March control 0.8 sap per g shoot IR64 IR B-B- B IR B-B- B IR B-B- B

36 Next for IR64 x Aday Sel NILs: 1. More detailed physiology work: How would smaller root and xylem diameter under drought result in improved yield? 2. Understanding effects of individual QTLs and different combinations of the 4 QTLs 3. Investigating leaf-related mechanisms of the IR64 x AdaySel NILs

Summary These results highlight that root traits can indeed contribute to improved rice yield under drought Multiple mechanisms (not just root traits) seem to be involved in the qdty 12.

37 Summary These results highlight that root traits can indeed contribute to improved rice yield under drought Multiple mechanisms (not just root traits) seem to be involved in the qdty 12.1 and IR64xAday Sel NILs The IRRI-drought approach (yield first, then traits) : allows us to be open-minded in our understanding of the mechanisms behind drought resistance; we are confirming that many mechanisms some unexpected can contribute to grain yield under drought Next: investigating GxE effects pyramiding of QTLs

39 Acknowledgements IRRI Drought Physiology Group Drought breeding group Funding: Generation Challenge Program Gates Foundation (STRASA) BMZ

MORPHO-PHYSIOLOGICAL ROOT TRAITS LINKED TO DROUGHT TOLERANCE IN CHICKPEA (Cicer arietinum L.)

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