IRRI Rice Seminar Series Current position Education and training

Jauhar Ali

Plant Breeder, Senior Scientist-I, GSR Project Leader & Regional Coordinator (Asia) for Development of Green Super Rice

Ph.D Genetics Indian Agricultural Research Institute, New Delhi, India (1993) M.Sc Genetics Indian Agricultural Research Institute, New Delhi, India (1990) B. Sc Agri (Hons) Punjab Agricultural University, Ludhiana, Punjab, India (1988)

Work experience
2011- Onwards Plant Breeder, Senior Scientist-I, Green Super Rice(GSR) Project leader, Regional Coordinator (Asia) for Development of GSR, PBGB, IRRI, Philippines 2009-2011 Scientist, Regional Coordinator (Asia) for Development of GSR, PBGB, IRRI, Philippines 2003-2009 National Coordinator, Hybrid & Molecular Rice Breeding Program of Iran (HMRBPI) & Consultant (IRRI-Iran project), Rice Research institute of Iran, Rasht, Iran 2000 -2003 Project Scientist, Genome Mapping Lab., PBGB, IRRI, Philippines 1995 -2000 Assistant Professor, Dept. of Crop Improvement, AC&RI, Tamil Nadu Agricultural University (TNAU),Trichy, India 1994 -1995 Research Fellow-1, Hybrid Rice (TGMS), PBGB, IRRI, Philippines 1993 -1994 Senior Research Associate, Rockefeller Rice Biotech Program on Anther culture & genetic transformation, IARI, Delhi

Research highlights
Publications: 3 Books and 50 Research Papers & articles Capacity Building: 7 MS, 2 PhD students, 1 OJT, 4 VRF completed; (now 1MS, 2PhD,1 OJT, 1VRF)-trained +723 researchers for seed production Breeding for resilience through development of green super rice materials for varied agro-climatic conditions and ecosystems Breeding for rice grain quality & yield -irrigated conditions-release of Bahar1 hybrid in 2009 &Gohar inbred variety in Iran in 2012 Heterosis breeding for irrigated and abiotic stress conditions through two and three line breeding approaches Breeding products (as team efforts) Bred 40 green super rice materials and nominated 18 entries in the Philippines, 1 aromatic entry and 10 entries in MET stage 2 Nominated 30 GSR inbreds and 24 inbreds in national trials of NARES (Asia) Bred eight TGMS lines (India)-1993, seven hybrids (India & Iran), one salt tolerant variety (India), three varieties (Iran) for irrigated Awards & distinctions: Pt. Jawahar Lal Nehru Award 1994 for outstanding PhD research in crop improvement; Tamil Nadu Young Scientist Fellowship 1997; IARI Junior and Senior Fellowship 1988 to1993; Punjab Agricultural University Merit scholarship holder 1984 to 88

Breeding for Resilience: Green Super Rice

IRRI

Drought tolerance Screening

Jauhar Ali
Plant Breeder, Senior Scientist GSR Project Leader PBGB, IRRI

Why there is a necessity for breeding for resilience?

Food Security 2008looming threat-higher yields under ever reducing resources Stable sustainable yields using lesser inputs(SSNM)-farmer practice-rainfed complex abiotic stresses-stressed irrigated condition- Lesser inputs-complex conditions Diseases & Insect pest threats-high input environments- Broad spectrum-durable R Caring for environment-pollution of water systems-chemical residues-Reduction of Cs Changing climatic situations-vulnerabilityheat-flooding-drought- Multiple Stress Tol.

Breeding for Resilience-GSR

Rice cultivars that produce higher and more stable yields with lesser inputs (water, fertilizers and pesticides)
High yielding GSR cultivars with Green traits: Resistances/ tolerances to: Abiotic stresses: Drought, salinity, alkalinity, iron toxicity, etc. Diseases: Blast, bacterial blight, sheath blight, viruses, and false smut etc Insects: Brown plant hopper, Green leaf hopper, etc Grain quality Mostly in elite RP background- later in RP-NARES

High resource-use efficiency: Water and nutrients (N P K)

Asia: Cambodia,Indonesia,Laos,Vietnam,Bangladesh,Pakistan,Sri Lanka Africa: Liberia, Mali, Mozambique, Nigeria, Rwanda, Senegal, Tanzania, Uganda China: Guangxi,Guizhou,Suchuan,Yunnan
GSR Materials given to NARES=Hybrids(193) + Inbreds (152)

TEST SITES: AFRICA & ASIA=15countries

Less inputs, more production & environment sustainability

Development of GSR materials by introgression breeding & designed QTL pyramiding (DQP) strategy initiated at IRRI in 1998
RP (3) x donors(205)
Li, Z.K. and Xu, J.L. (2007) Advances in Molecular Breeding Toward Drought and Salt Tolerant Crops Springer pp. 531-565.

F1s x RP

BC1F1s x RP

Self and bulk harvest

BC3F1s x RP Self and bulk x harvest

BC3F2 populations 1, 2, 3, 4, 5, 6,

Selection for target traits and backcrossing BC4F1s x

Bulk BC2F2 populations 1, 2, 3, 4, 5, 6,

BC4F2s

Screening for target traits such as tolerances to drought, salinity, submergence, anaerobic germ., P & Zn def., BPH, etc.
Confirmation of the selected traits by replicated phenotyping and genotyping of ILs for gene/QTL identification Crosses made between sister ILs having unlinked desirable genes/ QTLs for target ecosystem

DQP &MAS for pyramiding desirable genes/QTLs and against undesirable donor segments for target ecosystem

Development of GSR materials with improved target traits for wide scale testing in different ecosystems and its release. NILs for individual genes/QTLs for functional genomic studies

Ali et al (2006) FCR 97:66-76

~25 BC2F1s/donor x RP

Development of ILS for different abiotic and biotic stress tolerances at IRRI by 2004

Z.K. Li et al (2005) PMB 59:33-52; Ali et al (2006) FCR 97:66-76

Hidden diversity for abiotic and biotic tolerance in the primary gene pool of rice

Tremendous amounts of hidden diversity-BC progenytransgressive -target traits-regardless of donor performance-severe stress screening Common to identify in BC progeny-extreme phenotypes (tolerances) Selection efficiency highly dependent upon background Selection efficiency-affected by level of stress applied Selection efficiency for different target traits vary in BC generations. More distantly related donors, particularly landraces, tend to give more transgressive segregations for complex phenotypes in the BC progenies. Wide presence and random distribution of stress tolerance genes in primary gene pool of rice good news for rice breeders

Yu et al (2003) TAG 108:131-140; Ali et al (2006) FCR 97:66-76

Donors that gave better results with varying recurrent parental backgrounds
S.No. ST ZDT AG SUBT LTG BPH
MULTITRAITS

FAVOURABLE DONORS (VARY ACCORDING TO RP)

OM1706,OM1723,FR13A,NAN29-2,BABOAMI, KHAZAR TKM9,HEI-HE-AI-HUI(HHAH),JIANGXI-SI-MIAO(JSM), KHAZAR, MADHUKAR, SHWE-THWE-YIN-HYE (STYH), BASMATI385, IKSAN438, YU-QIU-GU, TETEP, NIPPONBARE, CO43, RASI, YUNHUI, BG304,BR24, FR13A GAYABYEO Y134,TKM9,KHAZAR,GAYABYEO,STYH,NAN29-2, BABOAMI,JSM,FR13A,OM1706 CISEDANE,FR13A,IR50,NAN29-2,OM1706,STYH,TAROM MOLAEI,TKM9,Y134 NAN29-2,GAYABYEO JSM,BABOAMI,TKM9,BG300,C418,LEMONT,MADHUKAR,MR167,OM1706,STYH, Y134 BABOAMI, GAYABYEO, SHWE-THWE-YIN-HYE (STYH), NAN29-2, FR13A, OM1706, KHAZAR, JIANGXI-SI-MIAO

Ali et al (2006) FCR 97:66-76

Designed QTL pyramiding experiments at IRRI

Experiment set I
IR64 x BR24 F1 x IR64 BC2F2 IR64 x Binam F1 x IR64 IR64 x STYH F1 x IR64 BC2F2 IR64 x OM1723 F1 x IR64 BC2F2 IR64 x Type3 F1 x IR64 BC2F2 IR64 x HAN F1 x IR64 BC2F2 IR64 x Zihui100 F1 x IR64 BC2F2

BC2F2

13 BC2F2 populations screened under two types of severe drought, resulting in 221 survived DT BC2F3 introgression lines (ILs), which were genotyped with SSR markers
IL1 x IL2 F1
X

Experiment set II

IL3 x IL4

IL7 x IL15 F1
X

F1
X

9 1st round pyramiding F2 populations from crosses between 15 ILs

F2

F2

F2

Screened under severe drought at the reproductive stage, resulting in 455 survived DT F2 plants, which were progeny tested and genotyped with SSR markers
(PL1 , PL2, PL3) x (PL4, PL5, PL6, PL7, PL8) F1s
X

Experiment set III

14 2nd round pyramiding F2 populations from crosses between 8 1st round PLs

F2s

Screened under severe drought at the reproductive stage and 667 survived DT F3 lines were progeny tested and genotyped with SSR markers

Ch.1
RM499 RM462 RM428 RM10287 RM323 RM84 RM220 RM86 RM283 RM522 RM1

Ch.2
Bin1.1 Bin1.2 Bin1.3 Bin1.4 Bin1.5 Bin1.6 Bin1.7
RM109 RM485 RM154 RM211 RM236 RM279 RM423 RM8 RM53 RM555 RM233A RM174 RM145 RM71 RM327 RM521 RM300 RM324 RM424 RM262 RM561 RM341 RM475

Ch.3
Bin2.1 Bin2.2 Bin2.3
RM545 RM245 RM517 RM60 RM81B RM22 RM523 RM569 RM231 RM175

Ch.4
Bin3.1 Bin3.2 Bin3.3 Bin3.4
RM307 RM401 RM537 RM551 RM335 RM518 RM261

Ch.5
Bin4.1
RM122 RM153

Bin5.1

RM204 RM540 RM469 RM587 RM588 RM190 RM589

Ch.6
Bin6.1 Bin6.2

Bin4.2

RM399 RM413 RM13 RM267 RM437

Bin5.2

RM272 RM490 RM575 RM576 RM259 RM243 RM583 RM600 RM572 RM581 RM580 RM23 RM129 RM329 RM446 RM562 RM594

Bin2.4
OSR13 RM14963 RM7 RM232 RM251

RM471

Bin4.3 Bin4.4

RM289 RM516 RM169

Bin5.3

RM510 RM204 RM585 RM584 RM557 RM111 RM225 RM314 RM253 RM50 RM549 RM539 RM136 RM19778 RM527

Bin6.3 Bin6.4 Bin6.5

Bin2.5

Bin3.5 Bin3.6

RM142

RM509

Bin5.4
RM598 RM163 RM164 RM291

RM3

RM454

RM9 RM5 RM306 RM488 RM237 RM246 RM473A RM11570 RM403 RM128 RM302 RM212 RM319 RM265 RM297 RM315 RM472 RM431 OSR23 RM14

Bin2.6
RM282 RM338

RM273 RM252

Bin4.5

RM161 RM188 RM19029 RM233B RM421 RM178 RM26 RM274 RM87 RM480 RM538 RM334

Bin5.5

Bin6.6
RM162

Bin3.7

RM241 RM470 RM303 RM317

Bin1.8

Bin4.6

Bin5.6

RM343 RM528 RM30 RM340 RM400 RM439 RM103 RM141 RM176 RM494

Bin6.7 Bin6.8 Bin6.9

RM106 RM263 RM526 RM221 RM525 RM318 RM450 RM497 RM6 RM240 RM530 RM112 RM250 RM166 RM197 RM213 RM48 RM207 RM266 RM535 RM138

Bin2.7 Bin2.8 Bin2.9

Bin1.9 Bin1.10 Bin1.11 Bin1.12 Bin1.13

RM156 RM411 RM487 RM16 RM347

Bin3.8
RM348 RM349 RM131 RM280

Bin4.7 Bin4.8

Bin5.7

RM504

RM567

Bin2.10 Bin2.11 Bin2.12

RM203 RM186 RM55 RM168 RM416 RM520 RM293 RM114 RM130 RM565 RM514 RM570

Bin3.9

RM559

Bin3.10

Bin3.11

STYH segments BR24 segments OM1723 segments Binam segments

FGUs identified in cross II-1 FGUs identified in cross II-2 FGUs identified in cross II-3 Cross III-1 Cross III-2 Cross III-3 Cross III-4

Li et al 2012 (unpubl)

RM227 RM85

Bin3.12

Ch.7
RM436 RM51 RM481

Ch.8
Bin7.1
RM408 RM506 RM407

Ch.9
Bin8.1
RM296 RM285 RM316 RM23818 RM444 RM219 RM524

Bin9.1

Ch.10
RM474 RM25022 RM25181 RM222 RM216 RM239 RM311

Ch.11
Bin10.1
RM181 RM286 RM4B RM26063

Ch.12
Bin11.1
RM20A RM4A

Bin12.1 Bin12.2

RM125 RM180 RM501 OSR22 RM214 RM418 RM432 RM11 RM346 RM182 RM336 RM10 RM351 RM455 RM505 RM234 RM18

OSR30 RM547

Bin9.2

Bin8.2
RM105 RM321

RM19

Bin7.2 Bin7.3

RM544

Bin10.2
RM332 RM167

Bin9.3 Bin9.4 Bin9.5

RM467 RM184 RM271 RM269 RM258 RM171 RM304

Bin11.2

RM247 RM512 RM179 RM101 RM277 RM511 RM519 RM313 RM309 RM463

Bin12.3

Bin7.4 Bin7.5 Bin7.6

RM25 RM126 RM407 RM44 RM72 RM137 RM331 RM339 RM342A RM515 RM223 RM284 RM210 RM556 RM447 RM256 RM149

Bin8.3

RM409 RM460 RM566 RM434

Bin10.3 Bin10.4 Bin10.5

RM120 RM479 RM202 RM536 RM260 RM287 RM209 RM229 RM457 RM187 RM21 RM473E RM206

Bin11.3

Bin12.4 Bin12.5 Bin12.6 Bin12.7

Bin8.4 Bin8.5 Bin8.6 Bin8.7 Bin8.8

RM257 RM108 RM242 RM278 RM201 RM107 OSR28 RM189 RM215

Bin11.4 Bin11.5 Bin11.6

Bin9.6 Bin9.7 Bin9.8

RM228 RM147 RM333 RM496

Bin10.6 Bin10.7

RM235 RM270

RM17

RM172 RM248

Bin7.7

RM230

RM245 RM205

RM254 RM224 RM144

RM264 RM281

Bin11.7

Genomic correspondences between FGUs identified in 150 ILs of 8 BC2 populations, 200 PLs of three 1st round pyramiding crosses and four 2nd round pyramiding crosses.

Zhang et al 2011 Dissecting genetic networks underlying complex phenotypes: Theoretical framework PLoS one 6(1) e14541

Putative genetic networks identified in 455 DT PLs derived from 9 crosses between DT IR64 ILs
A:
Drought

B:

Drought
AG2-1 (5) 0.994

I:

Drought

AG1-1 (7) 1.00

AL9-1 (3) 1.000

AG1-2 (7) 0.979

RM347 (3.8) 0.691

RM561 (2.6) 0.618

RM342 (8.5) 0.673

AG2-2 (6) 0.891

RM309 (12.5) 0.927

RM469 (6.1) 0.818

RM575 (1.4) 0.745

RM179 (12.3) 0.727

RM211 (2.2) 0.800

RM350 AG9-5(3) AG9-2(2) (8.4) 0.553 0.915 0.800

AG9-4 (5) 0.500

RM152 (8.1) 0.930

RM215 (9.7) 0.870

RM554 (3.7) 0.700

RM109 (2.1) 0.617

AG1-3 (13) 0.748

AG1-4 (4) 0.688

AG1-5 (5) 0.726

RM418 (7.3) 0.717

RM179 (12.3) 0.607

RM202 (11.3) 0.745

RM463 (12.5) 0.745

RM544 (8.2) 0.727

RM215 (9.8) 0.527

AG9-3(24) 0.870

RM446 (1.6) 0.830

D:

Drought

E:

Drought
RM543 (1.1) 1.000

G:

Drought
AG7-1 (18) 1.00

AG4-1 (6)
RM433 (8.7) 0.867 AG5-1 (12) 0.711

RM271 (10.4)

AG4-2 (4)

RM23 (1.5)

AG4-3 (4)

RM401 (4.1) AG5-4 (2) 0.767 0.733

RM298 (7.1) 0.767

AG5-2 (9) 0.809

RM53 (2.3) 0.833

RM85 AG7-5 RM286 RM44 (3.12) (2) (11.1) (8.3)

AG7-2 (2)

RM469 RM289 (6.1) (5.3)

AG7-7 (2)

RM36 (3.3)

AG7-3 (16)

RM516 (5.3)

RM245 (9.8)

RM18 (7.6)

RM215 RM544 RM272 RM179 RM441 (1.3) (11.2) (9.8) (8.3) (12.3)

AG4-4 (3)

RM220 (1.2)

RM222 (10.1) 0.567

RM270 (12.6) 0.567

RM17 (12.7) 0.500

RM424 (2.5) 0.667

RM244 (10.1) 0.583

RM101 (12.4) 0.766

AG5-3(2) 0.525

RM248 (7.7) 0.500

RM275 RM294B RM224 RM110 RM435 (11.7) (6.6) (1.6) (2.1) (6.1)

AG7-4 (7)

RM13 (5.2)

RM5 (1.7)

RM30 RM465A (6.8) (2.5)

F:

Drought

H:

Drought

AG6-1 (8) 1.000

AG8-1 (26) 1.00

C:

Drought
AG3-1 (4) 1.00

AG6-2 (5) 0.967

RM307 (2.1)

RM446 (1.6)

RM5 (1.7)

RM535 (2.12)

RM331 (8.4)

RM197 (6.1)

RM449 (1.6)

RM481

(7.1)

RM32 (8.3)

RM448 (3.10)

RM51 (7.1) 0.833

AG6-3 (12) 0.894

AG6-4 (2) 0.772

RM20 12.1 0.567

RM44 (8.3) 0.633

RM235 (12.6) 0.667

RM14 (1.13)

RM211 RM154 RM317 RM562 (2.2) (2.1) (4.6) (1.6)

AG8-3 AG8-4 (3) (3)

RM589 (6.1)

AG8-5 (2)

RM30 (6.7)

RM547 (8.3)

AG8-2 (2)

RM275 RM335 (3.12) (6.5)

RM143 (3.12)

RG8-6 (2)

AG3-3 (3) 0.736

AG3-2 (4) 0.855

RM302 (1.10) 0.782

RM172 (7.7) 0.727

RM258 (10.4)

RM246 (1.8)

RM169 (5.3)

RM245 (9.8)

Li et al 2012 unpubl.

6.5 6.0 5.5 5.0 4.5 2.5 4.0 1.5 3.5 0.5 3.0 0.0 0.5 1.0 1.0 2.0

Mean yield under the irrigated control (t/ha)

Type II (N=5) C: 5.710.42 VS: 1.360.38 RS: 2.200.45

IR64 (CK) C: 4.680.23 VS: 1.490.14 RS: 0.520.38 Type IV (N=7) C: 4.660.48 VS: 1.340.41 RS: 1.860.51
3.0

Type I (N=17) C: 5.760.53 VS: 2.070.55 RS: 1.790.47 Type III (N=19) C: 5.060.47 VS: 1.980.47 RS: 1.940.52

1.5

2.0

2.5

3.0

Mean yield performances (t/ha) of 48 2nd round PLs (4 types) as compared to IR64 (CK), under the irrigated control (C), drought stresses at the vegetative (VS) and reproductive stages (RS) in the 2007 and 2008 dry-season.
Guan et al. 2010 JXB

Highly salinity tolerant

GSR Drought tolerant pyramided lines in IR64 background

Under zero input conditions at IRRI DS2010

IRRI DT Check variety IR74371-70-1-1

GSR-IR83142-B-19-B

Wang et al 2010 Drought induced site specific DNA methylation JXB DOI:10.1093/jxb/erq391

DT PDLs AMMI-Biplot: 6
Entry No.
15 9 19 18 11 5 10 6 13 12 14 16 20 7 3 8 1 17 4 2

Locations -2011DS

BRAC-Gaz, VAAS-Gia, VAAS-Duo, ICRR-Jak, ICRR-Teg, & IRRI-Los Banos

GSR Lines
IR 83142-B-57-B IR 83141-B-17-B IR 83142-B-7-B-B IR 83142-B-79-B IR 83142-B-19-B IR 83140-B-11-B IR 83141-B-18-B IR 83140-B-28-B IR 83142-B-21-B IR 83142-B-20-B IR 83142-B-49-B IR 83142-B-60-B IR 83142-B-8-B-B IR 83140-B-32-B Best Check IR 83140-B-36-B 2nd Best Check IR 83142-B-61-B IR 74371-70-1-1 Apo

Mean LSD (t/ha) Group

5.46 5.17 5.13 5.12 5.06 5.05 5.02 4.94 4.86 4.79 4.78 4.75 4.74 4.74 4.67 4.32 4.29 4.27 3.57 3.53 a b bc bc bcd bcde bcdef bcdefg cdefg defg efg fg g g g h h h i i

10amBrGa PC %

17% adv.
0.5

1 60.9 2 24.7 1 17 10dsIRig

2 12 10 13 19 186

2nd Best Check

4
0.0

10dsIcJa 16 7 14 9 5

PC 2

Best Check
3
-0.5

10suVaGi 11 IR 83142-B-19-B 10suVaDu 15

IR 83142-B-57-B
20

IR 83140-B-11-B Environments

Mean LSD (t/ha) Group IL breeding + Designed QTL Pyramiding IRRI-Los Banos 6.55 a Possible role of Epigenetics VAAS-Gia 6.53 a 10dsIcTe VAAS-Duo 6.06 b Selection for grain yield, higher BRAC-Gaz 0.5 4.29 c spikelet fertility, deeper and thicker 0.0 -0.5 1.0 3.18 d roots esp. under reproductive stage ICRR-Jak PC 1 DT stress ICRR-Teg 2.08 e Why such yield advantages?
-1.0

Promising GSR Drought + Salinity tolerant materials tested under Iloilo during WS2010
GSR entry No of panicles Plant height (cm) Maturity (days) Yield (kg/ha) % increase over FL478 SES score 4WAT SES score Maturity

IR83140-B-11-B IR83140-B-28-B

16 13

84 86

116 114

1140 876

103.6 56.4

4 4

5 5

IR83140-B-32-B FL478
NSIC 222

15 11
19

85 70
83

114 111
112

657 560
147

17.3 0.0
-73.8

4 5
4

5 -

First two nominated for NCT Philippines WS2011

High protein 11%, AC 21%, GT-I, suitable for direct wet and dry, transplanting, drought, salinity, cold germination BLB, Blast tolerant

IR83140-B-11-B

PVS Purvakarta
2.5ha trial area Indonesia 8.2011

Grain yield t/ha

Site specific nutrient management (SSNM)

Untung et al (2012) unpubl.

Summary of GSR data received from NARES in Asia

No. of lines HYBRIDS INBREDS Batch 1 Batch 2 Batch 2 Batch 3 Batch 4 Batch 1 Batch 2 Batch 3 IRRI-GSR 24 80 42 37 9 22 31 9 47 IRLL, HY IRLL, HY RFLL, DT IRLL, DT, RFLL, (I & RFLL, I, RFLL (I & DT, SubT, HT, Nuse, J) DT, T-BL, J), DT, T- ST, HY T-BB, BL, GQ BL, BB, BPH, SB TBB, HT, WT, ST, GQ 15 14 5 10 8 4 21 17 5 12 11 3 16 14 5 39 21 7 31 18 6 10 8 4 Total 301 -

Line composition

Total no. of experiment reported No. of location Year/Season No. of data sets received from NARES No. of replicated data No. of data sets usable for GxE Analysis 5 Best Entries 1 2 3 4 5 Mean yield across location (t/ha) Average advantage over the best check Yield advantage of the best entry ANOVA: Pr(>F) ENV REP(ENV) GEN ENV:GEN

154 111 39 116 76 58

12 5
3

10 5
4

10 10
10

12 10
10 HuF1-9 HuF1-17

13 4
3

23 23
14

27 19
14 ZH1 TME80518

IIyou3203 HanF1-40 CXY2 CXY2 CXY727 ZXY673 XYR24 7.13 8.3% 13.3% 8.808E-09 0.0008013 <2.2e-16 <2.2e-16 HanF1-41 QS2

Zonghua 1 Luyin 46 HHZ BD007 SACG-4 RC8 4.21 -1.6% 7.9% SAGC-4

HanF1-27 IIyou623 HuF1-8 HanF1-36 Annong5 HuF1-4 HanF1-39 3LYR24 HuF1-13 5.83 5.49 6.17 22.1% 6.2% 28.8% 26.9% 13.1% 33.5% 2.334E-05 5.983E-08 <2.2e-16 1.763E-08 5.551E-16 <2.2e-16 <2.2e-16 <2.2e-16

926 FFZ SAGC-08 P35 SAGC-02 HHZ 5.09 5.26 8.7% 12.5% 12.8% 19.6%

1.143E-10 7.674E-06 <2.2e-16 <2.2e-16 <2.2e-16 0.723 7.58E-15 1.026E-07 <2.2e-16 1.206E-07 <2.2e-16 <2.2e-16 <2.2e-16 0.2526 <2.2e-16 <2.2e-16

List of the nominated GSR inbreds and hybrids for NCTs in the target SSA, SEA and SA countries
Mozambique Bangladesh Philippines

Sri Lanka

Indonesia

Lao PDR

Tanzania

Pakistan

Vietnam

Rwanda

Uganda

Senegal

Nigeria

Mali

Type of GSR lines in NCT trials Inbreds Hybrids Total

2
2 4

4
4 8

1
2 3

3
3 6

3
3 3 3

2
3 5

5
4 9

7
8

4
2

15

13 4

15

A total of 20 GSR inbreds and 21 hybrids have been nominated to the NCTs of the 8 target SSA countries; A total of 48 inbreds and 24 hybrids have been nominated in the NCTs of 8 Asian countries.

List of the promising widely adaptable GSR inbreds identified from adaptation yield trials in SSA, SEA and SA
Mozambique Cote Divoir Bangladesh Philippines Sri Lanka Indonesia Lao PDR Tanzania Pakistan Vietnam Rwanda Uganda Nigeria Mali

Name

All

HuangHuaZhan
Zhongzu14 ZH1 KCD1 RC8 Weed Tolerant 1

3
2

1
1 1

2
1 2

1
1 1 1 1 1

15
7

2 2

1 1 1 2 2 1

1 1

9 7

1
1

1
2

1
1

6 7

HUA-565
FFZ SAGC-4 WX763

2
1 2 2

2
1

1
1 2 1 1 1 1 1 1 1 1

5
5 7 5

HHZ developed in GAAS is a mega-variety of high yield & superior quality grown in 8 provinces of South & Central China (Guangdong, Jiangxi, Fujian, Hunan, Hubei, Anhui, Yunan and Guangxi).

The complex pedigree of Huang-Hua-Zhan (HHZ) involving 14 parents

Plant type, Panicle and Grain shape & size of HHZ & its immediate parents

S. C. Zhou et al., unpublished Z.K. Li et al 2012 (unpubl.)

P1(FHZ) P2(HXZ)

HHZ

P1(FHZ) P2(HXZ) HHZ

Genomic composition of the HHZ genome based on the re-sequencing data (From S. C. Zhou et al., unpublished)
Ch. 1 Ch. 2
Ch. 3 Ch. 4 Ch. 5 Ch. 6 Ch. 7 Ch. 8 Ch. 9 Ch. 10 Ch.11 Chr. 12

Each colored vertical line corresponds to a window of 10 kb. Vertical lines distribute upper side on each chromosome represent AZ haplotype blocks (red for 200kb AZ blocks, light red for <200kb AZ blocks) and QZ haplotype blocks (blue for 200kb QZ blocks and light blue for <200kb QZ blocks). Vertical lines distribute lower side on each chromosome represent Stress related QTL region (light yellow), Quality related QTL region (light green) and Yield related QTL region (light purple). Blue and red arrows indicate QZ blocks overlapped with Yield related QTL regions and AZ blocks overlapped with Quality related QTL regions, respectively.

IRRI-GSR breeding program & strategy

Two batches of 16 populations with the recurrent parent, HuangHua-Zhan (HHZ) and 16 donors from 9 different countries
Batch 1 1 1 1 1 1 1 1 2 2 2 Pop. HHZ5 HHZ8 HHZ9 HHZ11 HHZ12 HHZ15 HHZ17 HHZ19 HHZ1 HHZ2 HHZ3 Donor OM1723 Phalguna IR50 IR64 Teqing PSB Rc66 CDR22 PSB Rc28 Yue-Xiang-Zhan Khazar OM1706 Country of origin Vietnam (I) India (I) IRRI (I) IRRI (I) China (I) Philippines (I) India (I) Philippines (I) China (I) Iran (J) Vietnam (I) Gen.(12 DS) BC1F9 BC1F9 BC1F9 BC1F9 BC1F9 BC1F9 BC1F9 BC1F9 BC1F8 BC1F8 BC1F8

2
2 2 2 2

HHZ6
HHZ10 HHZ14 HHZ16 HHZ18

IRAT352
Zhong 413 R644 IR58025B Bg304

CIAT (upland)
China (I) China (I) IRRI (I) Sri Lanka (I)

BC1F8
BC1F8 BC1F8 BC1F8 BC1F8

GSR Introgression Breeding Procedure

06WS 08WS
Ist round selection

8 HHZ BC1F2 populations (08WS)

Yield traits DT screen 109DT plants ST screen 120ST plants SUB screen 15SUBT plants

Random plants

82HY plants

326 Genotyping/progeny testing for all target traits

09DS
2nd round selection 73HY ILs

326Yield

326DT screen

326ST screen

311SUB screen

47DT ILs

78ST ILs

171SUB ILs

QTL/Allelic diversity discovery for target traits

09WS
3rd round selection

369Genotyping/progeny testing for all target traits 108Preliminary yield trials under DT, low input, NC 68Promising ILs
3Demo 2NCT & 29 MET for 11WS

10DS
Selections can be continued if certain lines segregating

Confirming genetic networks for target traits and their genetic relationships

10WS/11DS 68 Replicated
yield trials

~80 promising ILs as parents for designed QTL pyramiding

06WS 09WS
Ist round selection

GSR Introgression Breeding Procedure 8 HHZ BC1F2 populations (09WS)

Yield traits
DT screen ST screen

SUB screen 21SUBT plants

Random plants

119HY plants

210DT plants

287ST plants

637Genotyping/progeny testing for all target traits

10DS
2nd round selection

Yield under NC & LI

420HY&FUE ILs

DT screen

ST screen

SUB screen

QTL/Allelic diversity discovery for target traits

180DT ILs

44ST ILs

221SUB ILs Confirming genetic networks for target traits and their genetic relationships

10WS
3rd round selection

865Genotyping/progeny testing for all target traits

Yield under NC & LI
HY&FUE ILs

11DS
Selections can be continued if certain lines segregating

DT screen

ST screen

SUB screen

DT ILs

ST ILs

SUB ILs ~80 promising ILs as parents for designed QTL pyramiding

11WS 12 DS

136 PYT
2 Demo

80 RYT

2 NCT & 11 MET 12DS

2nd Generation GSR materials

Multiple abiotic stress tolerant ILs developed from 16 donors into Huanghuazhan background and nominated to NCT using GSR breeding scheme.
Number of ILs
Produced from Selected at PYT Nominated to BN & RYT MET & NCT Drought tolerance (DT) 613 79 21 High yield under low-input (LI) 370 27 3 Salinity tolerance (SAL) 502 73 18 Submergence tolerance (SUB) 128 13 2 High yield under irrigated (Y) 576 100 27 DT+LI 246 15 2 DT+SAL 326 19 5 DT+SUB 82 6 DT+Y 382 40 11 LI+SAL 274 10 1 LI+SUB 38 0 LI+Y 178 1 SAL+SUB 60 9 SAL+Y 292 42 8 SUB+Y 101 5 1 DT+SAL+SUB 35 3 2 DT+SAL+Y 154 9 DT+SUB+Y 58 3 LI+SAL+SUB 20 0 LI+SAL+Y 117 0 LI+SUB+Y 36 0 SAL+SUB+Y 39 2 total: 845 146 40
IL=Introgression lines; BN=Backcross Nursery;PYT=Preliminary Yield Trial;RYT=Replicated Yield Trial; NCT=National Cooperative Testing (Philippines); Multi-environment testing (IRRI)

Target traits

Characterization of nominated GSR lines to the NCT Philippines

Designed QTL pyramiding (DQP)

DQP strategy for combining high yield(HY), drought tolerance(DT), salinity tolerance(ST) and submergence tolerance(SUBT) using the promising ILs as parental lines
IL1- HY, DT, SUB

X
F1

IL2- HY, DT, ST

F2

Yield traits

DT screen DT plants

ST screen ST plants

SUB screen SUBT plants

Random plants

HY plants

SNP Genotyping/progeny testing for all target traits

Group genotypes for different traits and their NILs

Farmers

New HYVs cultivars with DT,ST, SUBT for NCYT and PVS

Promising PLs for yield

Confirm genetic networks for different target traits and their genetic relationship

GSR Technology
GSR Technology
ILBreeding, DQP & PDLs

GSR
500 donors 56 RPs

Ideal RP BG
Ecosystem based approach
Screening of released GSR materials under target ecosystems Screening of already developed PDLs for abiotic stresses DT, ST, SUB, LI in the target ecosystems DQP for a trait & ecosystem related traits ILs, PDLs, DQP with adaptable RP BG for different target ecosystem

First Phase 2009-2012

Second Phase 2012-2018 Increase in success rate to develop highly adaptable genotypes for a given ecosystem

Rapid Visco Analyzer (RVA) Pasting properties of GSR lines in IR64 and HHZ RP backgrounds-suitable for varied consumers with different taste preferences
6000 120

1 3

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40

5000

5
100

7 9

4000 80

11 13
Temperature

Viscosity, cP

3000 60 2000 40 1000

15 17 19 21 23 25

0 0 -1000 Tim e, sec 100 200 300 400 500 600 700

20 800 0

27 29 31 33 35

AC=14.5-31.6%;GT=H-I-L;Protein=7.8-11.2

37 39

Blast evaluation of virulent strains

Evaluation of BB resistance of >500 lines (HHZ background) against 14 strains of 10 Xoo races, 2010 WS

Meirong Xu et al

HHZ

PSBRc66

BC1F5 # 329

BC1F5 #350

Zhongzu14-ski-4-1

BPH and Virus Resistance Screening

IRRI-ICRR joint project collaborators: Prof.Baehaki/Drs Muhsin,Untung
BC2 F3 HHZ populations screened against virulent BPH strain that caused outbreak in Sukamandi in 2010 Several populations showed ILs with comparable resistance with the checks in second round of screening. ICRR 8.2011

30 BC3F2 and BC2F3 population (CS 3) 39 BC3F3 and BC2F4 population (CS 4; 3rd year)ongoing

Resilient GSR products

HHZ12-DT10-SAL1-DT1- PVS trials (40 farmers) at Puypuy, Laguna ranked best over farmers check NSiC214 during WS2011 with preference score=0.118 against -0.0063(NSiC214)

High Yielding, Suitable for Direct seeding & Irrigated conditions, Aromatic, good cooking quality (AC24%, GT-L, Protein 9.4%) Drought and Salinity tolerant

IRRI bred GSR-HHZ 8-SAL6-SAL3-Y2 Breeding History

Combines earliness (105d), high yield in irrigated, low input, drought, salinity, submergence, direct seeded, transplanted, resistant to blast, BLB
Round 1 BC1F2 2008 WS HHZ 8 IG 9 SPS RF 13 SPS SAL 36 SPS SUB 0 SPS

>Promoted to MET2 (2012 DS)

RYT BC1F8 BC1F8 BC1F7 2011 WS HHZ 8-SAL6-SAL3-Y2 HHZ 8-SAL6-SAL3-Y1 HHZ 8-SAL6-SAL3-SAL1 Huang-Hua-Zhan NSIC Rc222 Irrigated Low-input Rainfed 5.88 4.41 3.95 3.09 4.71 3.90 2.99 3.00 2.92 2.95 5.24 3.46 4.38 3.56 5.17

Round 2 BC1F3

2009 DS HHZ 8-SAL6

IG 5.58

DT 2.25

SAL 41.67

SUB 36.36

Round 3 BC1F4

2009 WS HHZ 8-SAL6-SAL3

IG 4.40

RF 4.25

SAL 10.00

SUB 55.56

Apo
PYT BC1F5 BC1F5 2010 DS HHZ 5 SAL14-SAL2-Y2 HHZ 8-SAL6-SAL3-Y1 Huang-Hua-Zhan IR 72 Apo Irrigated Low-input Drought 7.75 6.66 7.58 6.99 6.94 2.77 1.94 3.31 3.08 3.23 2.11 2.45 2.49 2.53 3.07 MET1 BC1F7 2011 DS HHZ 8-SAL6-SAL3-Y2 IRRI Los Banos 3.48

3.98

3.47

3.60

Philrice CES 8.72

Philrice Isabela 7.74

Philrice Agusan 0.83

> Submitted to NCT (Transplanted Rice Category)

> Submitted to MET1 (2011 DS)
75% N 5.09 4.50 4.34 5.37 4.16 4.48 RYT BC1F7 BC1F7 2011 DS HHZ 8-SAL6-SAL3-Y2 HHZ 8-SAL6-SAL3-Y1 Irrigated Low-input Drought 7.00 6.05 3.11 2.75 0.81 0.86

PYT BC1F6 BC1F6 BC1F5

2010 WS HHZ 8-SAL6-SAL3-Y2 HHZ 8-SAL6-SAL3-Y1 HHZ 8-SAL6-SAL3-SAL1 Huang-Hua-Zhan NSIC Rc222 Apo

Irrigated Low-input Rainfed 5.32 5.59 4.67 4.89 5.35 4.71 4.17 3.31 3.94 4.20 4.78 4.77 5.32 4.75 5.57 4.42 4.94 5.52

BC1F6

HHZ 8-SAL6-SAL3-SAL1
Huang-Hua-Zhan NSIC Rc222 Apo

5.90
6.39 6.77 5.78

2.52
2.02 2.93 2.88

0.95
0.20 0.46 1.35

IRRI bred first generation of high yielding GSR materials

3-Season Data of HHZ Lines nominated to NCT 8.00 7.00 6.00
5.2 5.3 4.8 5.3 5.4 4.7 6.9 6.4 5.6 5.8 5.0 5.6 5.9 5.8 5.3 4.7 4.0 5.3 4.8 7.0 7.2

6.9 6.8
6.3 6.1 5.9

5.8

5.6

5.00

4.00
3.00 2.00 1.00 0.00

2010 WS

2011 DS

2011 WS

Mean

Seasonal Mean HHZ 5-SAL6-SAL3-DT1 APO

HHZ 12-SAL2-Y3-Y2 HHZ 5-SAL14-SAL2-Y2

HHZ 8-SAL6-SAL3-Y2 NSIC Rc222

Performance of IRRI bred GSR High Yield Potential Varieties under Irrigated Conditions
Grain Yield (t/ha) Designation HHZ8-SAL6-SAL3-Y2 Mestizo7 (Hybrid) HHZ12-DT10-SAL1-DT1 IR83142-B-7-B-B HHZ5-SAL10-DT1-DT1 IR72 HHZ5-DT8-DT1-Y1 HHZ8-SAL12-Y2-DT1 NSICRc158 HHZ12-Y4-DT1-Y1 IR83142-B-19-B IR83142-B-57-B IR83143-B-21-B HHZ8-SAL9-DT2-Y1 2010WS 6.55ab 5.68 bcde 6.75a 6.00 abcde 6.14abcd 5.96abcde 5.55 cde 6.43abc 5.86 bcde 5.57cde 5.12 e 5.48 de 5.16 e 5.78 bcde 2011DS 8.0ab 8.7a 7.2 bcde 7.6 bc 7.4 bcd 7.2 cde 7.6 bc 6.7 def 7.1 cdef 7.1 cdef 7.5 bcd 7.1 cdef 7.2 cde 6.4 defg Mean over seasons 7.28 7.19 6.98 6.80 6.77 6.58 6.58 6.57 6.48 6.34 6.31 6.29 6.18 6.09 % over IR72 10.56 9.27 6.00 3.34 2.89 0.00 -0.08 -0.23 -1.52 -3.72 -4.10 -4.41 -6.08 -7.45 % over NSICRc 158 12.27 10.96 7.64 4.94 4.48 1.54 1.47 1.31 0.00 -2.24 -2.62 -2.93 -4.63 -6.02

Plot size: 30sqm SSNM

HHZ5-SAL10-DT3-Y2
HHZ5-SAL10-DT2-DT1

5.69 bcde
5.47 de

6.3 fg
6.0 g

6.00
5.74

-8.89
-12.84

-7.48
-11.50

Reason:Higher HI, spikelets per panicle;panicles per sqm;total spikelets per sqm,CGR

An additional ton of rice in the rain-fed and irrigated lowlands will change the livelihoods of millions of resource poor farmers from the clutches of poverty and sustained income source to prosper.

THANKS

Acknowledgements & Thanks:

IRRI-CAAS-BMGF
Dr Zhikang Li Director GSR project
GSR National Coordinators (Asia) Drs Tuat, Untung, Rafiqul-Islam, Somphet, Nimal, Riaz and Arif, Makara,

Two public/NGO sectors:

Dr W.Xu (Boshima-SS,IDO) & Dr Sirajul Islam(BRAC) Dr C.X Mao GSR Training Consultant (CAAS-GAAS)

GSR-CAAS team: Drs Z. Li, Gao, Xu, Judy, Fu, Yu & many unknown contributors to the GSR materials
IRRI GSR team: Drs Nollie, Glenn, Choi, Redonna,Yamano,Andy,Krishna,Wang,Tao GSR-MBL team: Gelo; Corine, Lolit, Denver,
Macdo, Cenon, Keno, Deo, Eugene

Visiting Research Fellows: Drs Ma, Dr Uzokwe PhD: Zilhas, Meng; MS:Nina OJT: Shahana, Dilruba

GSR Project Adm.: Pauline; Secretarial Assistance: Badett

Cooperation & Collaboration makes the world a smaller place