Deploying Rice Varieties with Enhanced Adaptation to Lowland Farming Systems: Case Studies

from South AsiaAbdelbagi. M. Ismail, U. Singh, D. Platten, E.

Septiningsih, R. K. Singh, A. Kumar, D Mackill

Floods Salt stressDrought

International Rice Research Institute(IRRI) Philippines

‒ 90% of the world’s rice is produced and consumed in Asia‒ Over 70% of the world’s poor are in Asia

Poverty still the highest in rice producing countries

PovertyEach dot represents 250,000 people living on less than $1.25 a day, 2005

Rice ConsumptionAnnual consumption per capita

<12kg 12-36 36-72 72-120 >120kg

Rice consumption growing, but data poor,

Challenges and opportunitiesOver half the world’s rice area affected by

drought, flooding, salinity, nutritional deficiencies and toxicities

Most of the world’s poor rice farmers live in these areas

Future need have to be met from marginal lands and resources

Addressing abiotic stresses constraints facing today’s farmers will prepare us for future climate challenges

Grown from 50 oN in N. China to 35 oS in Australia and Argentina, From 3,000 m above sea level to 3 M below sea levelAdapted to diverse hydrology; from dry lands (upland rice), to flooded soils (lowlands), to deepwater (>6 m)Adapted to variable soils and temperature regimesExploiting this diversity will help cope with current and future food requirements

Rice is adapted to diverse soils and weather conditions

6 Jun 203

Need to explore the genetic diversity present in rice

IR64

IAC

16

5M

202

Mor

ober

kan

Dom

Suf

id

Cyp

ress

Pokk

ali

Asw

ina

Swar

na

Inia

Toc

uari

Co 39 Patbyeo Gerdeh Dular Sadu-cho

GRC (IRRI) holds over 124,000 accessions of cultivated rice & wild

relatives

Small proportion used in Breeding

Major abiotic stresses affecting rice

drought

submergence

salinity

Heat/cold

Other soil problems: Al & Fe toxicity and Zn & P deficiency

QTL Ch R2 LODSUB1 9 ~ 70% > 35Saltol 1 ~ 45% >8Pup1 12 ~ 80% 16.5

Drought 12 ~ 50% 35.0AG 9 >30% 19.9

Large-effect QTLs for abiotic stresses

SalinityGermination

under flooding

Pup1

P-def

+P -P

SUB1

Drought causes severe losses to farmers

Annually 25-30 m ha of rainfed rice experience droughtMajor QTLs for grain yield were identified and are being used in breedingNumerous tolerant varieties released during 2009-15 with yield advantage of 0.7 to 1.5 t/ha

Drought-stressed lowland riceWell-watered lowland rice

Case 1: Drought tolerant rice

Donors identifed & markers develped; being used for major QTLs in different genetic backgrounds

Recipient QTLs Chr Region Add. (%) DonorVandana qDTY12.1 12 RM28048-RM28166 42.8 Way RaremIR64 qDTY1.1

qDTY1.2

qDTY2.2

qDTY4.1

qDTY9.1

qDTY10.1

1 124 910

RM11943- RM12091RM212- RM315RM236- RM279RM335- RM518RM566- RM24350RM258- RM25694

24.317.413.66.328.918.0

N22N22

Aday selAday selAday selAday sel

Swarna qDTY1.1

qDTY2.1

qDTY3.1

12 3

RM11943- RM12146RM521- RM6374RM520- RM16030

29.322.730.2

N22ApoApo

Sabitri qDTY3.2

qDTY12.1

312

RM569-RM517RM28048- RM28199

31.122.9

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

MTU1010 qDTY1.1 1 RM11943- RM12146 16.1 N22

TDK 1 qDTY3.1

qDTY6.2

36

RM520-RM16030RM217

14.421.4

IR55419-04IR55419-04

Sahbhagi dhanNati mahsuri

Sahbhagi dhan

Moti

Nati Mahsuri

Sahbhagi dhan

Sahbhagi dhan

Neelkanth

Tolerant varieties showed positive impacts in farmers’ fields

Drought-tolerant varieties released in Asia during 2010-2014

Breeding line Year Designation CountryCRR 383-22 2008 CR dhan 40 IndiaIR 74371-70-1-1 2010 Sahbhagi dhan India

2011 BRRI dhan 56 Bangladesh2012 Sukha dhan 3 Nepal

IR74371-46-1-1 2012 Sukha dhan 1 NepalIR74371-54-1-1 2012 Sukha dhan 2 NepalIR 87707-446-B-B-B 2014 Sukha dhan 4 NepalIR 83383-B-B-108-3 2014 Sukha dhan 5 NepalIR 83383-B-B-129-4 2014 Sukha dhan 6 NepalIR81412-B-B-82-1 2011 NSIC Rc274 (Sahod Ulan 3) PhilippinesIR81023-B-116-1-2 2011 NSIC Rc 278(Sahod Ulan 5) PhilippinesIR72667-16-1-B-B-3 2011 NSIC Rc280 (Sahod Ulan 6) PhilippinesIR74963-262-5-1-3-3 2011 NSIC Rc284 (Sahod Ulan 8) PhilippinesIR 79971-B-191-B-B 2011 IR79971-B-191-B-B IndonesiaIR 79971-B-227-B-B 2011 IR 79971-B-227-B-B Indonesia

IR64+qDTY: First molecular breeding product reaching farmers

ENTRYRajshahi

Nepalganj RPR HYD SS HYD MS

Hazaribag Rewa

IR64 -DR 1525 3472 3956 1684 3800 1604 3731 IR 64 980 1597 2662 660 3085 958 2503

• Yield advantage of 0.6- 1.6 t/ha under drought• Similar yield and quality otherwise• Released in 2014 in India, Nepal, & Myanmar

• Lower canopy temperature• Higher RLD at depth in some soils• Higher root hydraulic conductivity

IR64IR64-2.2+4.1

Two QTLs: qDTY2.2 and qDTY4.1:

Case 2: Submergence tolerant riceFlash floods annually affect 15-22 million ha in Asia Affected areas are highly populated with poor farming communities FR13A identified in 1970s after screening 18,000 accessions SUB1 identified in mid-1990s as the major gene Cloned in 2005, gene-based markers developed and used in MABC

2006: Transferred into popular varieties using MABC

Sub1 varieties survive 10-18 days of submergence.

FR13A

Ten Sub1 varieties developed in backgrounds of popular varieties, all commercializedYield advantage: 1- >3 t/ha after 7-18 days of floodingNo penalty on yield or quality in absence of floods

Swarna-Sub1 in UP (Faizabad, India), 2008

After flood, July 31

After recoveryOctober 31

Breeding line Year designation CountryIR05F102 (Swarna) 2009 Improved Swarna India

2009 INPARA-5 Indonesia2010 BRRI dhan-51 Bangladesh2011 Swarna-Sub1 Nepal2011 Yemyoke Khan Myanmar

IR07F102 (IR64) 2009 NSIC Rc194 Philippines2009 INPARA-4 Indonesia

IR07F290 (BR11) 2010 BRRI dhan-52 BangladeshIR09F436 (Ciherang) 2011 INPARA-5 Indonesia

2014 BINA dhan11 BangladeshIR07F101 (S. Mahsuri) 2012 S. Mahsuri-Sub1 India

2011 S. Mahsuri-Sub1 Nepal2014 BINA dhan12 Bangladesh

CR1009-Sub1 2014 CR1009-Sub1 India

Several Sub1 varieties released in Asia: 2009-14

Ciherang-Sub1

Local varieties

Swarna-Sub1 Field submerged for 18 days in N. Bangladesh

Swarna

Field submerged for 22 days in, Kurigram,

Bangladesh

Over 4 m farmers reached with seeds of Sub1 varietiesWorks in all genetic backgrounds and environments Effective from seedling to early reproductive stage

Seedling-stage tolerance (12 dS/m)

Reproductive-stage tolerance (8 dS/m)

Case 3: salt-tolerant riceSalt stress affecting more than 16 m ha in AsiaEffect worsening with climate change, especially in coastal deltasTolerance is complex, involve several traitsTolerant landraces identified and are being used to breed tolerant varietiesMarkers developed for major loci and are being used for MABC and forward breeding

TolerantSensitive

Name Country released/year

Days to maturity

Grain type

CSR36 (Naina) India, 2005 135 Long slender

BRRI dhan47 Bangladesh, 2007 145 Medium boldBINA dhan8 Bangladesh, 2010 145 BoldBRRI dhan53 Bangladesh, 2010 122 Medium slenderBRRI dhan54 Bangladesh 2010 132 Medium slenderNDRK 5088 (ND Usar Dhan 2008)

UP, India 2010 120-125 Long bold

BRRI dhan 55 Bangladesh 2011 145 Long slenderCR Dhan 405 (Luna Sankhi) Odisha, India 2012 100-110 Medium bold

CR Dhan 406 (Luna Barial) Odisha, India 2012 150-155 Medium bold

BINA dhan10 Bangladesh 2012 121-125 Medium boldBRRI dhan61 Bangladesh 2013 145 Medium slenderGosaba 5 India 2014 135 Short BoldCSR 43 UP, India 2011/ 2014 110 Long Slender

BRRI dhan65 Bangladesh, 2014 100 Long slenderBRRI dhan67 Bangladesh, 2014 145 Medium slender

BRRI dhan73 Bangladesh 2015 120-125 Medium slender

Salt tolerant varieties released in India and Bangladesh

Salt tolerant varieties have considerable impacts in farmers’ fields

CSR-89IR-8

BRRI dhan28

BRRI dhan47

Before After

High yield in saline coastal & alkaline inlands(>2 t/ha)

Help reclaim salt affected areas

Slow; requires over 10-15 years to develop a new variety

Khandagiri

CR dhan 405

Alkaline soils, UP, India

Population Trait QTL Chr. Marker IM LOD IM R2

 IR29 x Pokkali Plant height qPH2 2 RM13332 5.1 16  Shoot Na/K qSNK1 1 RM10793 6.7 20  Root Na/K qRNK1     5.5 17Kalarata x Azucena SES 2 wk ses2w3.1 3 SO3065 7.2 18  Root length rl2.1 2 R2M50 9.1 22  Root DWt rdw1.1 1 RM7643 5.2 13  Shoot [Na+] snc1.1 1 RM10696B 7.7 19  Shoot Na+/K+ snkr1.1     9.7 23

Chikiram x Azucena SES Qses1.1 1 S01140 5.6 9.8

  Na+/K+ qNaK1.1 1 RM10748 12.4 20.5  [K+] qK1.1 1 RM10793 12.9 21.2  Root Na+/K+ qR-NaK1.1     5.5 9.6  Root [Na+] qR-Na6.1 6 RM340 5.1 9 Capsule x BR29 SES qSES3.1 3 R3M53 5.3 23  K+ uptake qK2.1 2 RM525 6.6 30  K+ uptake qK12.3 12 RM252B 5.9 15 FL478 x Azucena [Na+] qNa1.1 1 RM3252 7.5 16.9  SES final qNa1.3     9.7 21.2  SES initial qSES12.1 12 RM19 5.4 12.4

Examples of QTLs associated with salt tolerance e

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

1 32

4 5 6 7

8 9 10 11 12

32

4 5 6 7

8 9 10 11 12

32

4 5 6 7

8 9 10 11 12

32

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

2

4 5 6 7

8 9 10 11 12

4 5 6 7

8 9 10 11 12

4 5 6 7

8 9 10 11 12

4 5 6 7

8 9 10 11 12

4 5 6 7

8 9 10 11 12

4 5 6 7

8 9 10 11 12

5 6 7

8 9 10 11 12

5 6 7

8 9 10 11 12

5 6 7

8 9 10 11 12

6 7

8 9 10 11 12

6 7

8 9 10 11 12

6 7

8 9 10 11 12

6 7

8 9 10 11 12

7

8 9 10 11 12

7

8 9 10 11 12

7

8 9 10 11 12

7

8 9 10 11 12

7

8 9 10 11 128 9 10 11 128 9 10 11 128 9 10 11 128 9 10 11 129 10 11 1210 11 1210 11 1210 11 1211 1211 1211 12121212

Certain donors contribute novel QTLs

2.3.3.10 Salt stressVegetative stage- Saltol Reproductive stage CSR28/Sadri (RILs)

Chr 2 Chr 6

• K+ uptake in flag leaf on Chr2• Chlorophyll A, B

and total chlorophyll on Chr 6

• Number of unfilled grains on Chr 6

Examples of popular varieties introgressed with Saltol:

• BRRI dhan28• BRRI dhan29• BR11• IR64• AS966• Swarna

Strategy: combining QTL associated with tolerance

Identify donors contributing novel QTLsUse WGS to speed fine mapping, candidate gene discovery and marker developmentCombining several QTLs/genes from different sources for higher tolerance

Strategies for outreach:Over 30 varieties released in last 4 yearsFacilitate production and dissemination of sufficient high quality seeds to farmersAlign proper partners in the seed chain to facilitate multiplication and dissemination (>650 partners)– Strengthen the capacity of public & private sector

partnersMobilize additional resources (India: > 70 m US$)Launch awareness programs to speed uptakeCatalyze strategy dialogues to ensure enabling polices

STVs provide options for improved system-productivity

Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May REY(t/ha/yr)

Traditional/Farmers’ System Productivity : 2-9 t/ha/yr2-34-5

6-9

Improved System Productivity : 7-21 t/ha/yr8-10

7-9

13-1714-21

HYV Rice

Traditional Rice

Grasspea/MungTrad. RiceHYV Rice

HYV Rice

HYV Rice HYV Rice

HYV Rice HYV Rice Corn/Sflower/Wmelon

HYV Rice

HYV Rice Mung/Sesame

Sesame/Mungbean

Traditional Rice

Coastal zones of S. Bangladesh

LessonsStress tolerant varieties are delivering:

- Stability: higher yeilds and low variability in production- Equity: benefiting marginal and poor farmers forced to live off

marginal area at higher densities- Options for higher income – intensity & diversity Farmers accessing STVs (risk reduction):- Taking better care of their crop- Using more inputs, investing in better technologies- Accessing agricultural credit

Helped expanding in new areas not usable beforeGaining more support from national programs leading to fast delivery and impactsEntry for influencing national and regional policies on varietal release, seed guidelines & regional strategies

(BMZ)

UCRJulia-Bailey-Serres Takashi FukaoTim CloseHarkamal Walia

UCD:Pam RonaldEd Blumwald

IRRIVangie EllaTobias KretzschmarGina VergaraSudhanshu SinghYoichi KatoGlen Gregoreo

R&D PartnersPartners in Asia & AfricaStudentsGovernments NGOsPrivate CompaniesFarmers & Associations

Thank You