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

Amelia Henry

Colorado State Univ. Drought Symposium, 2012

Rice root types Root hairs

Root anatomy

lateral

nodal

IR64 Well-watered 12 days after sowing

seminal

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

Photo courtesy of B. Courtois

2000s • Drought breeding strategy: direct selection for yield under drought • Identification of QTLs for yield under drought

Major drought grain yield QTLs in the background of high yielding popular varieties

Recipient QTL (s) Chr. Region Add. (%) Donor

Vandana qDTY12.1 12 RM28048-RM28166 42.8 Way Rarem IR64 qDTY1.1

qDTY1.2 qDTY2.2

qDTY4.1 qDTY9.1

qDTY10.1

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 qDTY1.1

qDTY2.1

qDTY3.1

1 2 3

RM11943- RM12146 RM521- RM6374 RM520- RM16030

29.3 22.7 30.2

N22 Apo Apo

Sabitri qDTY3.2

qDTY12.1

3 12

RM569-RM517 RM28048- RM28199

31.1 22.9

IR77298-5-6-18 IR74371-46-1-1

MTU1010 qDTY1.1 1 RM11943- RM12146 16.1 N22 TDK 1 qDTY3.1

qDTY6.2

3 6

RM520-RM16030 RM217

14.4 21.4

IR55419-04 IR55419-04

Dhagaddeshi x Swarna Dhagaddeshi x IR64Dhagaddeshi x Swarna Dhagaddeshi x IR64

N22 × Swarna 30.20%

N22 × IR64 25.80%

N22 × MTU1010 16.90%

Dhagaddeshi × Swarna 24.80%

Dhagaddeshi ×IR64 8.55%

Additive effects in five populations for grain yield

under drought

DTY1.1: multiple donors - multiple backgrounds

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

IR64 x Aday Sel NILs 4 QTLs

Identification of physiological mechanisms behind drought-yield QTLs

Vandana x Way Rarem single QTL (qDTY12.1)

Planting

Drought stressed

Upland rice Lowland rice

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

Sequence for studying physiological mechanisms of drought tolerance in QTLs

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

Photos courtesy of Tess Sta Cruz

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

No differences in root growth at depth, but qDTY12.1 affected root diameter

2010DS uplandRoot length density

Soi

l dep

th (c

m)

10

20

30

40

50

60

IR84984-21-19-60-B (-)IR84984-21-19-62-B (-)IR84984-83-15-332-B (+)IR84984-83-15-481-B (+)VandanaWay Rarem

2010WS uplandRoot length density

Root length density (cm cm-3)

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

10

20

30

40

50

60

IR84984-21-19-62-B (-)IR84984-83-15-481-B (+)VandanaWay Rarem

2010DS uplandAverage root diameter

2010WS uplandAverage root diameter

Average root diameter (mm)

0.0 0.2 0.4 0.6

**

*

ANOVA p-valueQTL 0.05*Soil depth 0.05*QTL X soil depth 0.2ns

A. 2010DSupland 15-30 cm

IR84

984-

21-1

9-60

-B

IR84

984-

21-1

9-62

-B

none

IR84

984-

83-1

5-33

2-B

IR84

984-

83-1

5-48

1-B

Vand

ana

Way

Rar

em

Per

cent

of t

otal

root

leng

th in

dia

met

er c

lass

0

20

40

60

80

100

<0.05 mm0.05-0.1 mm 0.1-0.2 mm0.2-0.5 mm0.5-1.0 mm >1.0 mm

Root diameter:

**

*

***

-QTL +QTL parents

Distribution of root length within diameter classes

+QTL lines had a larger proportion of fine (lateral) roots than -QTL lines under drought

Hypothesis: greater root branching induced by drought stress in +QTL lines improves water uptake from drying soil

83-15-481-B-B (+QTL) 21-19-60-B-B (-QTL)

QTL 12.1: seedling stage greenhouse study

Detection of fine roots: Comair vs Winrhizo

<0.05 mm diameter

• +QTL lines had lower canopy temperatures and greater stomatal conductance during severe drought stress in the field

2010WS ROS Expt 2b QTL 12.1

30

31

32

33

34

35

36

37

38

28 31 36 42 56 70

days after sowing

Can

opy

tem

p (C

)

IR84984-21-19-62-B-B

IR84984-83-15-481-B-B

Vandana

Way Rarem

-QTL

+QTL

Rainout shelters: some evidence for a role of QTL 12.1 in water uptake

B. 2010WS70DAS

Stomatal conductance (mmol m-2 s-1)

140 160 180 200 220 240 260 280

Can

oy te

mpe

ratu

re (o C

)

30.0

30.5

31.0

31.5

32.0

32.5

33.0

- QTL+QTLVandanaWay Rarem

r2 = 0.25, p=0.12

A. 2010DS59 DAS

Stomatal conductance (mmol m-2 s-1)

0 50 100 150 200 250 300

Can

oy te

mpe

ratu

re (o C

)

32

33

34

35

36

37

38

39

r2 = 0.23, p = 0.02*

2010DS QTL 12.1 40cm

40

50

60

70

80

90

100

110

47 49 52 54 56 59 61 63 66 68 70 73 75

das

% o

f ini

tial s

oil m

oist

ure

afte

r re

wat

erin

g

+QTL

DD no sand

00.050.1

0.150.2

0.250.3

0.350.4

0.45

47 57 61 64 68 71

Wat

er u

ptak

e (g

/day

/cm

2 le

af)

IR84984-21-19-78-BIR84984-83-15-481-BIR90020:22-283-B-1IR90020:22-283-B-4VandanaWayRarem

DD sand

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

47 57 61 64 68 71

wat

er u

ptak

e (g

/day

/cm

2 le

af)

IR84984-21-19-78-BIR84984-83-15-481-BIR90020:22-283-B-1IR90020:22-283-B-4VandanaWayRarem

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?

Trials in lowland vs upland soils show different drought responses in terms of water uptake patterns

A. Trial 1

Days after sowing

56 58 60 62 64 66 68 70 72 74

Nor

mal

ized

wat

er u

ptak

e ra

te (k

g da

y-1 /

initi

al k

g da

y-1 )

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0AzucenaCypressDular FR13AIR64LTH

B. Trial 2

Days after sowing

78 80 82 84 86 88 90 92 94 96 98

C. Trial 3

Days after sowing

40 45 50 55 60 65 70

***

**

**

**

***

* **

Gowda et al. 2012 Functional Plant Biology

0.0

B. 2010 WS

Days after sowing

55 62 69 76

Wat

er u

ptak

e ra

te (g

d-1 c

m-2)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35IR86153-B1-B10-BIR86151-B1-205-BIR86153-B1-B11-BIR86151-B1-8-BIR86153-B1-604-BIR86153-B1-B6-BIR64DularSwarna

******

Kijoji et al. In review

Lowland soils: • consistent trends in water uptake across the drought period • water uptake under drought was correlated with root growth at depth

OryzaSNP

RAM x IR64

Genotypes adapted to upland soils: more rapid drydown regulation of transpiration

IRRI ICRISAT chickpea Zaman-allah et al., 2011

Drought-tolerant Drought-

susceptible

DD sand

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

47 57 61 64 68 71

wat

er u

ptak

e (g

/day

/cm

2 le

af)

IR84984-21-19-78-B IR84984-83-15-481-B IR90020:22-283-B-1 IR90020:22-283-B-4 Vandana WayRarem

CRURRS Hazaribag

Rajshahi, Bangladesh IGKV, Raipur

JNKVV, Rewa

NDUAT, Faizabad

ICAR, Tripura

Barwale Foundation DRR Hyderabad

TarharraHardinath

Nepalganj

Faizabad

Patna

Bihar Ag. Univ.

Hazaribag

Tripura

Rewa

Barwale Found.

Raipur

Next: Trials of NILs in a range of soil textures at target drought sites

• yield • root samples

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 qDTY12.1, such as transpiration efficiency

Vandana IR90020:22-283-B-4-B 83-15-481-B-B (+QTL) 21-19-60-B-B (-QTL)

Aday Sel x IR64 QTL lines

IR64 IR 87707-445-B-B-B IR 87707-182-B-B-B

CRURRS, Hazaribag, India 2011 WS

Performance of Aday Sel x IR64 QTL lines under drought

Aday Sel x IR64 NILs

+QTL 14-1-2-10

-QTL 14-1-2-13

IR64 -QTL

14-1-2-13

+QTL 14-1-2-10

Aday Sel NIL pairs show large differences in canopy temp under severe drought

+QTL 5-6-18

-QTL 5-6-11

Aday Sel

Oryza SNP panel: Canopy temperature was related to root length density

2010DS 15-30 cm

Root length density (cm cm-3)0.0 0.5 1.0 1.5 2.0 2.5

Can

opy

tem

pera

ture

(C

)

28

29

30

31

AzucenaDular IR64LTH

r2 = 0.40*

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

00.1

0.20.30.4

0.50.60.7

0.80.9

IR 64 IR77298-14-1-2-10

IR77298-14-1-2-13

IR 77298-5-6-18 IR77298-5-6-11

RLD

(cm

cm

-3)

30-45 cm45-60 cm

+ QTL - QTL + QTL - QTL

Root function for water uptake: hydraulic conductance

IR64

IR77

298-1

4-1-2-

10 (+

)

IR77

298-1

4-1-2-

13 (-

)

IR77

298-5

-6-18

(+)

IR77

298-5

-6-11

(-)

log

Sap

flux

at 5

00 k

Pa

(m3 s

-1)

1e-12

1e-11

1e-10

1e-9well-watered controldry-down from field capacitydry-down from 75% field capacity

Lower Lpr in + QTL lines from Aday Sel x IR64

14-1-2-10 (+ QTL) 14-1-2-13 (- QTL)

+ QTL lines had smaller root and xylem vessel diameters • only near the root tip, and only in the drought treatment

Hypothesis: smaller xylem vessel diameters in +QTL lines result in decreased xylem cavitation under severe stress

A. Henry, A. Cal, T. Batoto, R. Torres, R. Serraj. In Press. Journal of Experimental Botany

E. Exp 2b late metaxylem

WW DD DD-75%

late

met

axyl

em d

iam

. (m

)

30

32

34

36

38

40

42

DularIR64 KDML 105

wellwatered drought severe

drought

Dular and KDML decreased root xylem diameter with increasing drought stress

“Bleeding rate” measurements in the field: Dular and KDML showed consistently lowest bleeding rates compared to drought-susceptible varieties

C. Bleeding rate, Exp 1a control

Ble

edin

g ra

te (g

sap

g-1

sho

ot)

0.0

0.5

1.0

1.5

2.0

2.5

3.0

E. Bleeding rate, Exp 1a drought

Days after sowing

60 70 80 90 100 110

Ble

edin

g ra

te (g

sap

g-1

sho

ot)

0.0

0.5

1.0

1.5

2.0

2.5

3.0

DularIR42IR64KDML 105MoroberekanSwarna

Bleeding rates in IR64x Aday Sel NILs

Exp 4 March 14 2012 - stress

0.10.120.140.160.180.2

0.220.240.26

IR64 IR87707-445-B-B-B

IR87707-446-B-B-B

IR87729-69-B-B-B

sap

per g

sho

ot

Exp 4 March 14 2012 - control

0.40.450.5

0.550.6

0.650.7

0.750.8

IR64 IR87707-445-B-B-B

IR87707-446-B-B-B

IR87729-69-B-B-B

sap

per g

sho

ot

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 qDTY12.1 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

Funding:

Generation Challenge Program Gates Foundation (STRASA) BMZ

Drought breeding group