Colorado State Univ. Drought Symposium, 2012 Root traits behind major-effect drought-yield QTLs in rice Amelia Henry
Rice root types Root hairs nodal Root anatomy lateral seminal IR64 Well-watered 12 days after sowing
Rice has several different classes of roots, each with distinct diameters
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
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
Major drought grain yield QTLs in the background of high yielding popular varieties Recipient QTL (s) Chr. Region Add. (%) Donor Vandana qdty 12.1 12 RM28048-RM28166 42.8 Way Rarem IR64 qdty 1.1 qdty 1.2 qdty 2.2 qdty 4.1 qdty 9.1 qdty 10.1 1 1 2 4 9 10 RM11943- RM12091 RM212- RM315 RM236- RM279 RM335- RM518 RM566- RM24350 RM258- RM25694 24.3 17.4 13.6 6.3 28.9 18.0 N22 N22 Aday sel Aday sel Aday sel Aday sel Swarna qdty 1.1 qdty 2.1 qdty 3.1 1 2 3 RM11943- RM12146 RM521- RM6374 RM520- RM16030 29.3 22.7 30.2 N22 Apo Apo Sabitri qdty 3.2 qdty 12.1 3 12 RM569-RM517 RM28048- RM28199 31.1 22.9 IR77298-5-6-18 IR74371-46-1-1 MTU1010 qdty 1.1 1 RM11943- RM12146 16.1 N22 TDK 1 qdty 3.1 3 qdty 6.2 6 RM520-RM16030 RM217 14.4 21.4 IR55419-04 IR55419-04
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 IR64 25.80% N22 MTU1010 16.90% Dhagaddeshi Swarna 24.80% Dhagaddeshi IR64 8.55% Vikram et al. 2011, BMC Genetics 2011
Drought Research at IRRI IRRI Climate Unit
Rainout shelters and sensor rack for NDVI and IRT S. Klassen
IRRI Greenhouse lysimeter facility ~1m-tall PVC cylinders Simultaneous measurements of water uptake and leaf area
Root sampling in the field
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 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
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
No differences in root growth at depth, but qdty 12.1 affected root diameter 10 2010DS upland Root length density 2010DS upland Average root diameter 20 30 ** Soil depth (cm) 40 50 60 10 2010WS upland Root length density IR84984-21-19-60-B (-) IR84984-21-19-62-B (-) IR84984-83-15-332-B (+) IR84984-83-15-481-B (+) Vandana Way Rarem * 2010WS upland Average root diameter 20 30 40 IR84984-21-19-62-B (-) IR84984-83-15-481-B (+) Vandana Way Rarem ANOVA p-value QTL 0.05* Soil depth 0.05* QTL X soil depth 0.2ns 50 60 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 0.0 1.6 0.2 0.4 0.6 Root length density (cm cm -3 ) Average root diameter (mm)
Distribution of root length within diameter classes Percent of total root length in diameter class 100 80 60 40 20 0 A. 2010DS upland 15-30 cm Root diameter: <0.05 mm 0.05-0.1 mm 0.1-0.2 mm 0.2-0.5 mm 0.5-1.0 mm >1.0 mm IR84984-21-19-60-B IR84984-21-19-62-B * ** * ** none IR84984-83-15-332-B IR84984-83-15-481-B Vandana Way Rarem -QTL +QTL parents
QTL 12.1: seedling stage greenhouse study +QTL lines had a larger proportion of fine (lateral) roots than -QTL lines under drought 83-15-481-B-B (+QTL) 21-19-60-B-B (-QTL) Hypothesis: greater root branching induced by drought stress in +QTL lines improves water uptake from drying soil
Detection of fine roots: Comair vs Winrhizo <0.05 mm diameter
Canopy temp (C) Rainout shelters: some evidence for a role of QTL 12.1 in water uptake 38 37 36 35 34 33 32 31 30 +QTL lines had lower canopy temperatures and greater stomatal conductance during severe drought stress in the field 110 -QTL 2010WS ROS Expt 2b QTL 12.1 +QTL 28 31 36 42 56 70 days after sow ing 2010DS QTL 12.1 40cm IR84984-21-19-62-B-B IR84984-83-15-481-B-B Vandana Way Rarem Canoy temperature ( o C) 39 38 37 36 35 34 33 33.0 32.5 Stomatal conductance (mmol m -2 s -1 ) A. 2010DS 59 DAS r 2 = 0.23, p = 0.02* 32 0 50 100 150 200 250 300 B. 2010WS 70DAS % of initial soil moisture after rewatering 100 90 80 70 60 50 40 +QTL 47 49 52 54 56 59 61 63 66 68 70 73 75 das Canoy temperature ( o C) 32.0 31.5 31.0 30.5 - QTL +QTL Vandana Way Rarem r 2 = 0.25, p=0.12 30.0 140 160 180 200 220 240 260 280 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? DD no sand Water uptake (g/day/cm2 leaf) 0.45 0.4 0.35 0.3 0.25 0.2 0.15 0.1 0.05 0 47 57 61 64 68 71 IR84984-21-19-78-B IR84984-83-15-481-B IR90020:22-283-B-1 IR90020:22-283-B-4 Vandana WayRarem DD sand water uptake (g/day/cm2 leaf) 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 IR84984-21-19-78-B IR84984-83-15-481-B IR90020:22-283-B-1 IR90020:22-283-B-4 Vandana WayRarem 47 57 61 64 68 71
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 ) 3.5 3.0 2.5 2.0 1.5 1.0 0.5 Azucena Cypress Dular FR13A IR64 LTH *** ** 0.0 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. 2012 Functional Plant Biology Water uptake rate (g d -1 cm -2 ) 0.35 0.0 0.30 0.25 0.20 0.15 0.10 B. 2010 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 0.05 0.00 55 62 69 76 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
Genotypes adapted to upland soils: more rapid drydown regulation of transpiration DD sand water uptake (g/day/cm2 leaf) 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 47 57 61 64 68 71 IR84984-21-19-78-B IR84984-83-15-481-B IR90020:22-283-B-1 IR90020:22-283-B-4 Vandana WayRarem Droughttolerant Droughtsusceptible IRRI ICRISAT chickpea Zaman-allah et al., 2011
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
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 83-15-481-B-B (+QTL) 21-19-60-B-B (-QTL) IR90020:22-283-B-4-B Vandana
Aday Sel x IR64 QTL lines
Performance of Aday Sel x IR64 QTL lines under drought IR 87707-445-B-B-B IR 87707-182-B-B-B IR64 CRURRS, Hazaribag, India 2011 WS
Aday Sel x IR64 NILs +QTL 14-1-2-10 -QTL 14-1-2-13
Aday Sel NIL pairs show large differences in canopy temp under severe drought IR64 -QTL 5-6-11 -QTL 14-1-2-13 +QTL 5-6-18 +QTL 14-1-2-10 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 = 0.40* Azucena Dular IR64 LTH 28 0.0 0.5 1.0 1.5 2.0 2.5 Root length density (cm cm -3 ) Henry, Gowda, Torres, and Serraj, 2011, Field Crops Research
Aday Sel NIL pairs did not show large differences in root length density at depth Expt 4s Aday Sel ROS 0.9 0.8 0.7 RLD (cm cm -3 ) 0.6 0.5 0.4 0.3 0.2 30-45 cm 45-60 cm 0.1 0 IR 64 IR77298-14-1-2- 10 IR77298-14-1-2- 13 IR 77298-5-6-18 IR77298-5-6-11 + QTL - QTL + QTL - QTL
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 IR77298-14-1-2-10 (+) IR77298-14-1-2-13 (-) IR77298-5-6-18 (+) IR77298-5-6-11 (-)
+ QTL lines had smaller root and xylem vessel diameters only near the root tip, and only in the drought treatment 14-1-2-10 (+ QTL) 14-1-2-13 (- 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. 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
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) 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. Bleeding rate, Exp 1a drought 0.0 60 70 80 90 100 110 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 0.1 IR64 IR87707-445-B- B-B IR87707-446-B- B-B IR87729-69-B-B- B Exp 4 March 14 2012 - control 0.8 sap per g shoot 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 IR64 IR87707-445-B-B- B IR87707-446-B-B- B IR87729-69-B-B- B
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 12.1 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
Acknowledgements IRRI Drought Physiology Group Drought breeding group Funding: Generation Challenge Program Gates Foundation (STRASA) BMZ