2012 gsr - breeding technology

GSR Breeding Strategy – Exploiting the

Hidden Reservoir of Diversity for

Improving Complex Traits in Rice

Zhi-Kang Li/CAAS

GA biosynthetic pathway

KS

GA15

GA24

GA44

GA19

GA12 -aldehyde

Geranylgeranyl

ent- Copalyl diphosphate

ent -Kaurene

ent -Kaurenol

ent -Kaurenal

ent -Kaurenoic acid

ent -7a-hydroxy

GA12

GA9

GA53

GA20

KO

KAO

GA

GA3ox

GA4 GA1

GA7ox

GA13ox

kaurenoic acid

diphospate

C20ox

AS

CPS

KS

KO

KAO

sd-1

HLONG

Stamp

Subjects

� Concept of GSR

� Introduction

� Perspectives

� GSR Breeding Strategy and

Technology

HLONG

Stamp

The impact of ‘Green Revolution’ in ChinaYield

Impact of ‘Green Revolution’

30000

40000

50000

60000Impact of hybrid rice

Yield/unit area

Total production

Yield

0

10000

20000

1965

1967

1969

1971

1973

1975

1977

1979

1981

1983

1985

Year1988

1990

1992

1994

1996

1998

2000

2002

Important problems in rice

production worldwide

• Increasing problems in abiotic and biotic

stresses

• Over-use of pesticides • Over-use of pesticides

• Abuse of chemical fertilizers

• Shortage of water

• Ever increasing demands for yield increase

• Urgent need for improved quality

Total grain production（（（（in

unit area yield Fertilizer application and grain production in China

4000

4500

70000

75000

Fertilizer use

Current agricultural practices: higher inputs-for high yields- polluted

environments

China consumes ~1/3 of the global production of chemical fertilizers

and pesticides annually on only 7% of the world’s cultivated lands

In China

Fertilizer use (in 10000t)

Total grain production

10000 t

）、

）、

）、

）、unit area yield

(kg/10ha））））

0

500

1000

1500

2000

2500

3000

3500

4000

1975 1978 1982 1985 1988 1991 1994 1997 2000

15000

20000

25000

30000

35000

40000

45000

50000

55000

60000

65000Fertilizer use

Grain production

Grain yield per unit area

25

30

35

40

3035404550

6

7

90

110

130

150单产农药化肥

（（（（million ton

））））

10000 ton

））））

Trends of rice production and uses of pesticides

and fertilizers in China in the last 30 years

ton/ha））））

0

5

10

15

20

1975 1978 1981 1984 1987 1990 1993 1996 1999 2002 200551015202530

3

4

5

1978 1981 1984 1987 1990 1993 1996 1999 2002 200510

30

50

70

90

Fertilizers

（（（（

Pesticides

（（（（10000

Yield

（（（（ton/ha

350 350

Grain yield(ton/hm2)

Grain yield/ha

1

2

3

4

5

1961 1966 1971 1976 1981 1986 1991 1996 2001 2006

/

Grain yield per unit area

0

50

100

150

200

250

300

350

1961 1966 1971 1976 1981 1986 1991 1996 2001 2006

氮肥

用量

（公

斤/

公顷

）

0

50

100

150

200

250

300

350

氮肥

生产

效率

（kg/k

g）

氮肥用量

PFP

Nitro

gen

consu

mption(k

g/h

m2)

Nitro

gen

use

effic

iency

(kg/k

g )

N consumption

NUE

1961 1966 1971 1976 1981 1986 1991 1996 2001 2006

350

300

250

200

150

100

50

0

350

300

250

200

150

100

50

0

Annual yield losses

� ~20% from abiotic stress: drought,

problem soils, etc) problem soils, etc)

� ~15% from biotic stress: diseases

and insects, even with the heavy

uses of pesticides.

Water crisis and

drought in China

� Fresh water resources per capita in China is less than a

quarter of the world average;

� Agriculture uses ~70% of the fresh water in China, and

rice uses ~70% of the fresh water used in agriculture;

� Drought is occurring more frequently than ever before;

� Great yield loss of rice to drought in major rice areas.

4.0

5.0

6.0

Yield (t/ha)

Irrigated(40%)

Largely Irrigated

Which places have been left out by Green

Revolution: Rice Yield Gaps in Irrigated and

Rainfed Ecosystems in Asia, 1967-97

80

100

Irrigated Rainfed

0.0

1.0

2.0

3.0

1967 1970 1973 1976 1979 1982 1985 1988 1991 1994 1997

Year

Yield (t/ha)

Rainfed(30%)

Largely Irrigated

(30%)

Source: M. Hossain, IRRI

0

20

40

60

MC TC

Adoption percentage

of modern cultivars

Consequences of the Green Revolution

ProductivityProductivity

DiversityDiversity

Less inputs, more production, and

environmental sustainability

少投入、多产出、保护环境少投入、多产出、保护环境少投入、多产出、保护环境少投入、多产出、保护环境

Chinese scientists are calling

“Second Green Revolution”

少投入、多产出、保护环境少投入、多产出、保护环境少投入、多产出、保护环境少投入、多产出、保护环境

- to develop and widely adopted “Green Super

Rice” that can produce high and stable yields

under less inputs (chemical fertilizers,

pesticides and water, and stress resilient).

What are “GSR”?

High yielding cultivars with multiple “Green” traits:

Resistances/ tolerances to:

Abiotic stresses: Drought, salinity, alkalinity, etc.Abiotic stresses: Drought, salinity, alkalinity, etc.

Diseases: Blast, bacterial blight, sheath blight,

viruses, and false smut etc

Insects: Brown plant hopper, stem borer, etc

High resource-use efficiencies: Water and nutrients (N, P)

Many target traits:

Yield and its related traits

Stability

To develop GSR rice varieties, breeders

are facing the following challenges:

Stability

- Resistances to biotic stresses

- Tolerances to abiotic stresses

Quality

- Eating, cooking, and milling

- Micronutrients

Where are the sources

of genetic variation

for improving the

‘green’ traits?

Rice Germplasm Collections in

Genebanks Worldwide: ~ 215,000 entries

27% of

modern

10% of 22 wild species

90% of the

Cultivated rice73% of

landraces

varieties

Everson et al. 1998

Status of the International Rice

Genebank Collection at IRRI

AccessionsIncoming

samplesTotal

O. sativa 85,999 15,784 101,783

O. glaberrima 1,333 288 1,621

Wild species 3,970 495 4,465

Total 91,302 16,567 107,869

Characterization of O. sativa

accessions (n=79,925)

Characterization of O. sativa

accessions (n=79,925)

7070

8080

9090

100100

% accessions scored

% accessions scored

00

1010

2020

3030

4040

5050

6060

7070

% accessions scored

% accessions scored

44 morpho-agronomic traits44 morpho-agronomic traits

20,00020,00020,00020,000

30,00030,00030,00030,000

40,00040,00040,00040,000

50,00050,00050,00050,000

Evaluation of rice germplasm for stress

resistance/tolerances at IRRI

Evaluation of rice germplasm for stress

resistance/tolerances at IRRI

Screened Resistant

accessions

accessions

20,00020,00020,00020,000

10,00010,00010,00010,000

Blast

Blast

Bacterial

Bacterial

blight

blight

Sheath

Sheath

blight

blight

Rice tungro

Rice tungro

BPH 1

BPH 1

BPH 2

BPH 2

BPH 3

BPH 3

Green

Green

leafhopper

leafhopper

Whitebacked

Whitebacked

planthopper

planthopper

Cold

Cold

tolerance

tolerance

No.accessions

No.accessions

Cold tolerance (1-3 = tolerant; 5 =

intermediate; 7-9 = susceptible)

Cold tolerance (1-3 = tolerant; 5 =

intermediate; 7-9 = susceptible)

2,000

2,500n=6,625n=6,625

0

500

1,000

1,500

1 3 5 7 9

15

20

25

Yield responses of the 193 parental lines of IRMBN

to the terminal drought under the lowland condition

-19.1±±±±44.0%

0

5

10

15

-100 -80 -60 -40 -20 0 20 40 60 80 100 120 140 160

Yield reduction (in %)

Core collections of rice, wheat, corn and

soybean were established with only 5% of

the accessions representing over 90%

genetic diversity of the whole collections. 0.1

Jap. M.

Jap. U.

Jap. L.

Ind. EM.

Ind. M.

Ind. MLJaponica

Indica

0.1

�� Establishment of the core collections for

major crops in the CAAS’s genebank

Comparison of genetic diversity among core collections

with different sampling ratio

Basic Collections Core Collection Mini-core

Accessions Entries sampling % Representation Entries sampling % Representation

Rice 61479 3074 5% 89.9% 300 0.5% 66.6%

Wheat 23135 1160 5% 90.1% 231 1.0% 69.1%

Soybean 28809 1439 5% 91.0% 280 1.0% 71.0%

(Jia jizheng,2004)

Current Status of Characterization and Utilization of

Germplasm Collections in Genebanks Worldwide

- Phenotypic evaluation and description

To identify accessions with desirable (often extreme)

� Collection and conservation largely completed

� Characterization – very superficial

To identify accessions with desirable (often extreme)

phenotypes to be used as parents in breeding programs

How much valuable genetic variation for target traits in

the primary gene pool for breeding remains unclear!

- Few accessions with desirable phenotypes for most traits

- No accessions with desirable phenotypes for certain traits

Reasons for Poor Utilization of Germplasm

� Outstanding commercial genotypes are commonly

destroyed by crosses with unimproved exotic germplasm

� Utilization – very poorly

- Less than 5% of the collected germplasm in the Genebanks

have been utilized in the worldwide breeding programs

destroyed by crosses with unimproved exotic germplasm

(Duvick 1984)

� Selection of parental lines in breeding programs are largely

based on phenotype and very few accessions appear to have

“desirable” phenotype for complex traits

� Slow but consistent genetic improvement can still be

achieved even within a narrow base in many breeding

programs

� To exam if there is sufficient (novel) genetic

variation for target traits in the primary gene

Objectives

The GSR Breeding Strategy: Exploiting

the maximum genetic diversity in the

primary gene pool of rice

variation for target traits in the primary gene

pool for most complex traits

� If yes, to develop an effective and efficient strategy

to exploit the genetic diversity for complex traits

- Generation of information and training personnel

- Integration with the molecular tools

- Integration with gene discovery

Full Exploitation of The Genetic Diversity in the

Primary Gene Pool of Rice

The Basic Idea

The GSR Breeding StrategyDonors

(203 WMCC, 300 CMC +

20 wild rice accessions)

Recipients(46 best commercial

Varieties and hybrid parents)

X

BC breeding to introgress

superior alleles from MCC into

elite genetic backgrounds

Trait-specific

IL sets in elite GBs

Genotyping by re-

sequencing of all

parents

Molecular database

of the parents

Genotyping &

Parents for next

round of DQP

Genotyping &

phenotyping

Genetic characterization

of ILs

Development of

new cultivars

and PL setsBreeding by MRS

or DQP

Release to

farmers

-omics and

bioiformatics

Theory and

technology of

breeding by

molecular design

Gene networks and metabolic

pathways of the target traits and

functional diversity of alleles at the loci

The Chinese GSR research institutions - China

National Rice Molecular Breeding Network

Goal

The goal of NCMBN was to develop

superior inbred and hybrid crop

cultivars with significantly improvedcultivars with significantly improved

yield stability, yield potential, and

grain quality for the major rice

growing areas in China.

Specific objectives

� To broaden the genetic base of crop cultivars in major crop

growing areas of China by maximizing the gene flow from the

primary rice gene pool into elite genetic backgrounds through

backcross breeding;

� To exploit the hidden diversity of the primary rice gene pool

for improving complex target traits;for improving complex target traits;

� To develop IL sets for important traits in elite rice genetic

backgrounds;

� To discover and characterize large numbers of QTLs and

QTL networks underlying important traits, and to mine

allelic diversity at important QTLs;

� To establish genetic/phenotypic database for the ILs;

� To train a new generation of molecular rice breeders in China.

Proof of the Concept

• How much useful genetic diversity,

particular for the complex

phenotypes, within the primary

gene pool of rice?

Two Fundamental Questions:

gene pool of rice?

• Can we combine the process of

breeding with gene discovery

(gene/QTL discovery and allelic

mining)?

Part I: Introgression breeding

and mass selection

Recurrent Parents

IR64 - Indica, high yield/widely adaptable

New Plant Type - Japonica, high yield potential

Teqing - Indica, high yield/widely adaptable

The “value” added and base broadening

approach – Introgression breeding

Widely

adaptable

high yield

Add new genes/traits

by backcross breedingIR64 introgression

lines with improved

target traitshigh yield

varieties (IR64)

target traits

Discovery of desirable QTLs using

DNA markers and MAS for

pyramiding QTLs

IR64 lines with improved

target traits and the “same”

yield potential and quality

Procedure of the backcross breeding for development of ILs for

gene/QTL identification and cultivar development

RP x donors F1s x RP 25 BC1F1s x RP

~25 BC1F2s x RP

Bulk BC1F2 populations

~25 BC2F1s x RP

Self and bulk

harvest

Self and bulk

harvest

X

1, 2, 3, 4, 5, nScreen for

target traits:

X

Bulk BC2F2 populations

1, 2, 3, 4, 5, n

Large numbers of ILs with selected target traits in the elite RP genetic background

Replicated progeny testing for the introgression lines (ILs) for the selected target traits (tolerances to

drought, salinity, submergence, BPH, etc), and for yield performances and other agronomic traits under

non-stress conditions

Best ILs with selected target trait(s)

used as parental lines for

pyramiding genes/QTLs from

different donors

Genotyped w/ DNA markers to track the gene

flow and to identify genes/QTLs for the target

traits

Promising ILs with selected target

trait(s) and good yield performances

nominated for NCTs

Development and releases of

green super rice cultivars for

specific target environments

To rice farmers in the target

environments

Four Major Groups of Target Traits

� Tolerances to abiotic stresses (drought,

salinity, low and high temperatures, N

and P use efficiency, etc.)

� Resistances to biotic stresses (blast, � Resistances to biotic stresses (blast,

sheath blight, false smut, BPH, stem

borer, BB, etc.)

� Yield potential and heterosis

� Quality parameters

Donor gene pool (203 accessions from

34 countries)

Sub-G1 (54)

Sub-G2 (6)

Sub-G3 (33)

Sub-G4 (46)

I (indica)

Sub-G4 (46)

Ba-Bao-Mi (Yunnan)

Sub-G5(15)

Sub-G6 (12)

Sub-G7 (28)

Sub-G8 (9)

Jalmagna (India)

II (japonica)

III (New group)

Europe

NA

America Others

15%NA

Europe America Others

10%

Proportions of accessions

from different geographic

regions

Relative genetic diversity of

accessions in different

geographic regions

Gene diversity of the donor gene pool

SA

33%China

22%

SEA

30%

NA

SA

40%China

26%

SEA

24%

NA

Target traits

• Tolerances to drought, salinity, submergence,

zinc deficiency, phosphorus deficiency,

anaerobic germination, etc.

• Resistances to BB, BPH, blast, tungro, sheath • Resistances to BB, BPH, blast, tungro, sheath

blight, etc.

• Different maturities

• Different types of grain quality parameters

• Yield and related traits

BC Breeding Procedure

RP Donors of diverse originsX

F1s

BC1F1

X RP

X RP

BC F

Selection for target traits

Survival plants GenotypingProgeny testing

x

BC2F1

BC2F2 bulk populations

Major differences of introgression breeding and

the conventional BC breeding

BC breeding Marker aided

BC breeding

Introgression

breeding

RP selection Elite Same Same

Donor selection Yes Yes No/diverse

Target traits Single Single or few No limitationTarget traits Single

monogenic/dominant

Single or few No limitation

Selection Mass selection MAS Mass selection

Progeny testing yes yes yes

Pop. size Small Small Regular

Selection efficiency High High Depends

Breeding efficiency Low Low High

Selection strategy for target

traits in random BC

progeniesprogenies

Stress for 20 days (March 27,2001) Stress for 56 days (May 2, 2001)

Screening of BC2F2 populations for tolerance

to terminal drought at the reproductive stage

under the lowland conditions

Variation in BC2F2 populations for drought

tolerance under the lowland conditions

Summary of selected drought tolerant BC2F2 plants

under lowland stress conditions

Total plants selected

NPT IR64 Teqing

897 2775 489

Total

4161

# of selected plants

per population

8.5

(3.8%)

22.4

(10.0%)

6.3

(3.0%)

13.2

(6.8%)

Range

No. of I donors

0 - 85 0 - 100 0 - 30 0 - 100

59 67 59 185

per population (3.8%) (10.0%) (3.0%) (6.8%)

No. of J donors 32 45 19 96

No. of populations 113 124 105 320

Contributing donor (%) 80.5 90.3 74.3 87.8

The Screening of BC2F2 populations

under upland drought conditions

The RP, IR64


IR64 Teqing

192 334

Total

526



Ave. selected plants

Per population9.6 (4.6%) 10.8 (5.2%) 10.3 (5.0%)

Range

No. of I donors

4 - 20 3 - 15 4 - 30

12 23 35

No. of J donors 8 8 16

No. of populations 20 31 51

Contributing donor (%) 100 100 100

Parental performances and 442 selected DT BC2F2plants for drought tolerance from 19 BC populations

VG Donors IR64 (S) Teqing (M) NPT(SS)

I BR24 (S) 14 (27) 12 (7) 3

I STYH (S) 20 (26) 4

I OM1723 (S) 7 (17) 7 (6) 0

TotalOrigin

Bangladesh

Myanmar

Vietnam

29 (34)

LL (UL) LL (UL) LL

24 (26)

14 (23)

-

J FR13A (SS) 15 (16) 17 (15) 0

J Type3 (SS) 23 (15) 10 (12) 0

J Binam (M) 20 (19) 14 (13) 1

J HAN (M) 11 (13) - 3

Zihui100 (S) 8 - 9I

Total

Khazar (S)J

India

India

Iran

China

China

Iran

32 (31)

33 (27)

35 (32)

14 (13)

58 58

17

176 (133) 60 (53) 22 256 (186)

-

Screening of BC2F2 populations for salinity

tolerance at the seedling stage

ST CK

Pokali

Young seedlings were subjected to:

6 dSm-1 for 3 days, 12 dSm-1 for 2 weeks, 18

dSm-1 for 1 week, and 24 dSm-1 for 1 week

IR64

Confirmation by progeny testing

Seedling screening at EC 24 dSm-1 for 3 weeks

Table 1. Summary results of BC populations for screening salinity tolerance

Details BC2F2 screening BC2F3 reconfirmation

IR64 Teqing NPT Total IR64 Teqing NPT Total

Total BC2F2 populations 62 58 55 175 24 34 10 68

Single plant selections per BC

population 4 - 12 4 - 13 1 - 14 0 - 43 0 - 49 0 - 11

Total selected BC2F3 lines 490 428 374 1292 448 392 21 861

Selection intensity (%) 3.95 3.69 3.40 3.69

Number of indica donors 47 47 42 136 20 27 7 54

Selected lines 369 345 289 1003 372 269 21 662


Number of japonica donors 9 9 7 25 3 6 1 10

Selected lines 70 66 44 180 43 123 0 166


Number of intermediate donors 4 1 3 8 1 1 2 4

Selected lines 35 5 19 59 33 0 0 33


BC2F2 screening BC2F3 reconfirmation

# of BC2F2 pop. 62 58 55 175 24 34 10 68

# of selections per pop. 4 - 12 4 - 13 1 - 14 1 - 14 0 - 43 0 - 49 0 - 11


Summary results of BC populations

for screening salinity tolerance

# of selections per pop. 4 - 12 4 - 13 1 - 14 1 - 14 0 - 43 0 - 49 0 - 11

Total selected lines 490 428 374 1292 448 392 21 861

# of contributing

donors 60 57 52 169

SI (%) 3.95 3.69 3.40 3.69

For individual BC populations of 200 plants, a difference of 4% between two populations in

selection intensity (survival rate) is statistically significant at P < 0.05 when the selection

intensity is between 0.1 and 0.5.

Screening of BC2F2 populations for

submergence tolerance in a deep-water pond

Thirty-five-day old seedlings were submerged under deep water

for two weeks, then allowed to recover

# of BC pop. 47 47 36 130 60 57 62 179

Anaerobic germination Submergence


Summary results of BC populations

for screening anaerobic germination

and submergence tolerance

# of BC pop. 47 47 36 130 60 57 62 179

# of selections per pop. 0 - 5 0 - 6 0 - 14 0 - 15 3 - 13 0 - 12


# of contributing

donors 46 46 35 127 59 57 60 176

SI (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93

Screening of BC2F2 populations for

anaerobic germination

Direct seeding then submerged under 10 cm-deep water

Summary results of BC populations screened for anaerobic

germination and submergence tolerance

Details Anaerobic germination Submergence




population 0 - 5 0 - 6 0 - 14 0 - 15 3 - 13 0 - 12


Selection intensity (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93 Selection intensity (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93


Selected lines 31 67 77 175 538 431 451 1411

Selection intensity (%) 0.43 0.90 3.10 0.84 1.15 0.86 0.90 0.96


Selected lines 11 14 31 56 83 52 63 198



Selected lines 5 0 7 12 40 0 16 56


Screening for BPH Resistance

IR64

Summary results of BC populations screened for low temperature

germination and brown planthopper resistance

Details Low temperature germination Brown planthopper resistance

IR64 TQ NPT Total IR64 TQ NPT Total



population 0 - 21 0 - 18 0 - 31 0 - 22 0 - 22 0 - 2



Number of indica donors 1 1 0 2 49 60 49 158Number of indica donors 1 1 0 2 49 60 49 158

Selected lines 0 3 0 3 565 221 2 788



Selected lines 55 52 39 146 54 21 0 75



Selected lines 24 22 12 58 33 2 0 35


For individual BC populations of 100 plants, a difference of 2.5% between two populations in selection

intensity (survival rate) is statistically significant at P < 0.05 when the selection intensity is < 0.1.

# of BC2F2 pop. 14 15 10 39 64 74 62 200


Low temperature germination BHP resistance


Summary results of BC populations for screening

low temperature germination and BPH resistance



# of contributing

donors 14 14 10 38 62 67 59 189

SI (%) 5.64 5.13 5.10 5.31 10.19 3.81 0.03 4.71

For individual BC populations of 200 plants, a difference of 4% between two populations in

selection intensity (survival rate) is statistically significant at P < 0.05 when the selection

intensity is between 0.1 and 0.5.

Screening for tolerance to phosphorus

deficiency

Tested in natural conditions in Pangil, Laguna.

Screening for tolerance to zinc deficiency

Summary results of BC populations screened for zinc deficiency tolerance

Details BC2F2 screening under moderate field stress

BC2F4 progeny testing under very severe

field stress


Total number of BC populations 51 42 36 129 11 21 10 42


population 4 - 12 2 - 12 0 - 12 0 - 12 0 - 10 0 - 15 0


Selection intensity (%) 7.42 7.60 7.50 7.50 2.14 2.41 0.00 2.01 Selection intensity (%) 7.42 7.60 7.50 7.50 2.14 2.41 0.00 2.01


Selected lines 370 320 237 927 63 200 0 263



Selected lines 63 63 84 210 0 55 0 55


Number of intermediate donors 3 - 1 4 1 0 0 1

Selected lines 21 - 9 30 9 0 0 9

Selection intensity (%) 5.83 - 7.50 6.25 5.63 0.00 0.00 5.63

Selection for changed grain

type of Teqing

Selection for high

yield

High tiller number

Screening for blast resistance

Low N stress

experiment

under rain-off

shelter

Improving japonica for cold

tolerance at the reproductive stage

Donor parent Subspecies CodePopulation

size

No. of

selected

plants

SI 1

(%)

SF (%)

Mean ± SD2 Range

Bg90-2 Indica A 450 41 9.1 63.3±8.4D 50.3-86.5

X21 Indica B 450 29 6.4 64.3±9.9CD 50.6-87.1

X22 Indica C 450 28 6.2 65.6±10.1BCD 50.7-87.3

Screening results of 11 CY1 (recurrent parent) BC2F4 backcross populations for cold

tolerance at the booting stage in 2008 (1 SI = selection intensity, SF = spikelet

fertility; 2 Different letters indicate statistical significance at P < 0.05, based on the

Duncan testing)

X22 Indica C 450 28 6.2 65.6±10.1BCD 50.7-87.3

Q5 Indica D 450 31 6.9 71.1±11.1ABC 50.9-91.4

Chhomrong Japonica E 450 24 5.3 75.6± 51.4-87.8

Doddi Indica F 450 25 5.6 71.0±10.0ABC 50.2-90.0

Fengaizhan Indica G 450 44 9.8 74.1± 52.2-98.5

Shennong265 Japonica H 450 21 4.7 69.2±11.4ABCD 50.7-93.8

Yuanjing7 Japonica I 450 41 9.1 71.1±9.8ABC 50.0-90.1

OM997 Indica J 450 21 4.7 72.1±9.1AB 54.9-89.6

Cs94 Indica K 450 19 4.2 64.2±8.6CD 51.4-86.0

Mean 450 29.5 6.5 69.2±4.2

CY1 Japonica 324 24.8±4.3E 19.0-30.0

Screening of the BC2F4 bulk populations for cold tolerance

(CT) at the booting stage:

Seeds of the BC2F4 bulk populations were sown in the seedling nursery on April

15, 2008, and 450 40-day old seedlings of each BC2F4 bulk population were

transplanted into a 45-row plot with 10 plants in each row and a spacing was

25×15cm in the sheltered water pond of JAAS on May 25. Two rows of CY1

were also transplanted on both sides of each plot as the checks. The water-pond

were irrigated with water of normal temperature (25~28℃). When CY1 entered

℃℃℃℃

were irrigated with water of normal temperature (25~28℃). When CY1 entered

the stage of panicle initiation, the LT treatment was initiated by irrigation of

flowing cold water (19±±±±0.5℃℃℃℃), which was adjusted in a nearby water pool by mixing cold underground water (9℃℃℃℃) with the river water. The depth of the

cold water in the pond was 20cm and the treatment was maintained for ~30

days until panicles of almost all plants exerted completely. Then, irrigation

with normal temperature water was resumed until the maturity. At the

maturity, all plants except those with >3 days earlier heading or those with

>3 days delayed heading than CY1 were harvested for measuring the

spikelet fertility. Under this LT treatment, CY1 had a spikelet fertility of

24.8±±±±4.3%, then, any plant with spikelet fertility >50% were selected.

Donor parent

No. of

selected

lines

Cold stress at the seedling

stage Cold stress at the reproductive stage

Survival rate of seedlings

(%) SNP FGN SF (%)

Mean Range Mean Range Mean Range Mean Range

BG90-2 41 19.5 10.0~62.5 114.5 76.3~164.2 55.0 22.1~95.7 48.0 18.5~71.3

X21 29 19.4 11.1~40.3 99.7 73.3~125.0 50.5 29.5~90.3 50.3 30.9~74.9

X22 28 19.6 12.5~40.7 113.2 70.3~139.0 58.5 4.5~94.9 51.4 5.6~79.4

Q5 31 18.3 15.0~33.8 114.6 68.3~185.4 56.5 15.3~113.6 49.2 14.6~83.6

Evaluation of 324 BC2F6 introgression lines and their recurrent parent, CY1 for cold

tolerance of at the seedling and booting stages in 2009 (SNP = spikelet number per panicle,

FGN = filled grain number per panicle, SF = spikelet fertility)

Q5 31 18.3 15.0~33.8 114.6 68.3~185.4 56.5 15.3~113.6 49.2 14.6~83.6

Chhomromg 24 17.0 15.0~32.5 109.8 77.6~175.2 74.0 47.0~104.8 66.9 45.6~83.4

Doddi 25 17.3 12.5~25.0 112.9 89.4~182.6 73.9 51.5~108.5 65.4 48.7~80.6

Fengaizhan 44 16.7 12.5~25.0 96.5 70.2~115.1 67.1 14.3~96.0 70.1 12.7~86.1

Shennong265 21 15.6 0.0~23.3 96.9 65.0~144.8 62.0 36.9~99.2 63.0 40.0~79.9

Yuanjing7 41 18.5 15.0~45.0 116.0 93.5~151.0 80.6 30.4~106.4 69.2 25.5~84.2

OM997 21 37.1 15.0~82.4 81.6 56.2~108.1 42.0 14.9~64.0 51.1 23.3~72.0

Cs94 19 22.3 15.0~42.5 113.3 82.0~137.9 69.5 31.8~99.4 60.0 34.2~75.5

CY1 14.8 10.8~20.0 106.6 98.6~114.6 36.7 32.7~40.8 35.1 33.7~36.5

LSD0.05 4.5 8.3 8.2 6.2

PopulationN1

The reproductive stage The seedling stage

FGN SNP SF (%) SR (%)

Code Donor N1 N2 N1 N2 N1 N2 N1 N2

A BG90-2 41 18 0 13 6 17 1 5 0

B X21 29 7 0 0 3 15 0 4 0

C X22 28 17 2 8 1 17 3 5 0

D Q5 31 15 2 10 4 20 3 1 0

E

Comparison of selection efficiencies of 11 CY1 BC2F6 populations for cold

tolerances at the seedling and reproductive stages

E Chhomromg 24 17 0 7 3 22 0 2 0

F Doddi 25 23 0 1 0 24 0 0 0

G Fengaizhan 44 35 1 0 7 42 1 0 0

H Shennong265 21 12 0 2 9 18 0 0 1

I Yuanjing7 41 40 0 9 0 40 0 3 0

J OM997 21 2 1 0 13 13 0 14 0

K Cs94 19 14 0 5 1 14 0 6 0

Total 324 200 6 55 47 242 8 40 1

1 N is the total number of selections based on single plant spikelet fertility (SF) in BC2F4 populations from Table 1, N1 and N2 are the numbers of the BC2F6 lines

showing significantly higher or significantly lower than CY1 for the measured traits. FGN, SNP, SF and SR are filled grain number per panicle, spikelet number

per panicle, spikelet fertility and survival rate of seedlings.

Trait 1 Chhomrong Doddi Fengaizhan Shennong265 Yuanjing7 Mean CK

N 24 24 24 20 24 116

Under the normal conditions

PH (cm) 135.2±±±±4.4 130.6±±±±5.8 125.7±±±±5.4 127.2±±±±3.7 132.3±±±±4.5 130.3 117.1

BM (g/plant) 37.1±3.3 36.5±3.4 38.1±3.5 33.5±3.3 35.1±2.4 36.2 34.7

FGN 143.4±15.0 143.7±17.2 148.1±12.3 135.1±15.6 156.3±±±±19.4 145.7 138.9

SNP 176.6±20.8 179.4±20.9 171.2±17.4 172.9±17.7 197.2±±±±21.8 179.7 168.6

SF (%) 81.6±6.6 80.4±8.1 86.9±±±±5.8 78.4±7.2 79.2±5.3 81.4 82.4

GY (g/plant) 19.4±±±±2.94 20.5-3.0 20.9±±±±2.5 18.7±±±±2.5 18.7±±±±2.7 19.6 19.7

HI (%) 55.0±5.2 59.1±4.9 57.9±3.7 59.1±4.4 56.0±4.8 57.3 60.3

PN 5.4±0.6 5.7±0.4 5.7±0.6 5.6±0.7 4.8±±±±0.5 5.5 5.7

Mean performances of 116 ILs of five populations for 11 traits evaluated under

normal and cold water stress conditions in 2010

PN 5.4±0.6 5.7±0.4 5.7±0.6 5.6±0.7 4.8±±±±0.5 5.5 5.7

GW (g) 24.3±1.5 26.3±±±±1.6 22.0±±±±2.1 24.5±1.1 26.3±±±±1.4 24.7 24.9

HD (d) 113.9±3.3 113.0±4.1 116.3±6.0 112.5±4.7 113.6±3.9 113.9 111.1

Under the cold water stress

PH (cm) 118.1±±±±7.9 119.9±±±±7.7 119.8±±±±7.7 122.4±±±±6.6 125.2±±±±5.7 121.0 107.8

BM (g/plant) 16.2±3.2 16.1±2.7 16.8±2.5 15.3±3.6 17.5±3.6 16.4 12.0

FGN 46.8±28.4 39.1±20.2 63.8±±±±14.3 22.9±±±±14.1 46.4±19.8 44.5 12.8

SNP 118.9±23.9 121.7±13.8 110.4±12.9 117.7±24.1 139.6±19.6 121.8 121.5

SF (%) 38.8±18.3 32.3±14.5 57.3±±±±10.3 19.7±±±±12.1 33.3±14.6 36.9 10.5

GY (g/plant) 3.5±±±±2.2 3.0±±±±1.7 5.0±±±±1.3 1.9±±±±1.2 3.6±±±±1.9 3.5 1.0

HI (%) 33.3±7.6 30.7±6.7 40.9±±±±4.4 25.8±±±±7.2 30.8±5.1 32.5 25.1

PN 3.3±0.5 3.4±0.6 3.3±0.5 3.7±0.9 3.2±0.5 3.4 3.5

GW (g) 17.9±1.5 18.0±1.6 17.5±2.7 17.1±0.9 17.9±1.3 17.7 16.4

HD (d) 131.3±2.2 128.2±3.3 132.0±4.1 126.9±4.1 128.6±3.0 129.5 125.2

Donor N1 TreatBM (g/plant) FGN

GY

(g/plant)

GW

(g)

HD

(d)

HI

(%)

PH

(cm)PN

SF

(%)SNP

N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2

Chhomrong 24

S

18 0 18 0 14 0 15 0 24 0 14 0 19 2 3 8 21 0 6 12

Doddi 24 18 0 19 0 15 0 16 1 16 2 14 2 21 0 5 7 19 0 4 4

Fengaizhan 24 22 0 24 0 23 0 6 3 22 1 24 0 20 0 2 6 24 0 0 12

Shennong26

5 20 12 1 7 0 6 0 5 2 10 8 7 6 18 0 9 5 10 0 6 8

Yuanjing7 24 21 0 21 0 19 0 17 0 16 0 15 1 24 0 3 8 20 0 12 1

The numbers of ILs from the 5 populations that deviated significantly CY1 for 11

measured traits evaluated under cold water stress (S) and normal (N) conditions in 2010

Total 116 91 1 89 0 77 0 59 6 88 11 74 9 102 2 22 34 94 0 28 38

Chhomrong 24

N

15 2 11 5 9 8 4 13 13 2 1 16 24 0 3 9 7 9 11 4

Doddi 24 11 4 10 5 9 5 17 4 11 3 6 7 24 0 4 4 8 12 13 5

Fengaizhan 24 16 0 14 2 9 1 2 20 19 3 3 15 21 0 5 7 15 4 8 8

Shennong26

5 20 3 8 5 7 2 9 5 10 8 7 5 7 20 0 8 10 5 13 9 7

Yuanjing7 24 5 3 17 2 5 14 18 2 11 3 3 18 24 0 0 21 4 12 20 1

Total 116 50 17 57 21 34 37 46 49 62 18 18 63 113 0 20 51 39 50 61 25

1 N is the total number of ILs with CT selected from each population; N1 and N2 are the numbers of the ILs showing significantly higher and lower trait

values than CY1.

GY = grain yield, BM = biomass, PH = plant height, PL = panicle length, PN = panicle number per plant, FGN = filled grain number per panicle, SNP =

spikelet number per panicle, SF = spikelet fertility, HD = heading date, GW = 1000-grain weight, HI = harvest index.

Line# Pop.12010 under the normal condition 2010 under cold water stress 2009 under stress

PH BM SNP SF GY HI PN GW HD PH BM SNP SF GY HI PN GW HD SNP SF SR

CK(CY1) 117.1 34.7 168.6 82.4 19.7 60.3 5.7 24.9 111.1 107.8 12.0 121.5 10.5 1.0 25.1 3.5 16.4 125.2 106.6 35.1 14.8

LW213 G134.2 48.5 192.3 91.1 28.1 60.1 6.4 22.8 103.0 129.2 19.5 131.2 69.1 7.2 46.8 3.5 15.7 128.0 101.7 81.2 12.5

LW164 F126.5 45.7 204.5 87.8 28.5 65.2 6.4 23.5 117.0 118.8 17.2 120.0 27.3 2.5 26.0 3.3 16.1 129.0 113.2 56.9 15.0

LW180 F131.7 38.8 182.0 89.8 23.4 63.1 5.7 25.6 101.0 131.7 18.0 138.0 39.6 4.9 36.3 3.3 19.1 123.0 107.3 68.0 17.5

LW157 F133.4 41.0 218.7 71.9 23.4 59.9 6.0 25.2 116.0 114.8 20.9 132.8 40.1 5.0 33.8 4.3 17.1 131.0 110.6 60.3 17.5

LW170 F129.3 40.0 183.3 83.7 22.8 59.7 5.9 24.0 117.0 117.8 19.6 119.5 45.5 5.3 38.4 4.8 16.7 131.0 118.4 71.9 17.5

LW214 G122.0 38.0 159.8 85.6 22.9 63.5 6.7 17.9 120.0 108.5 14.3 103.7 54.9 4.5 44.4 3.3 16.3 137.0 86.7 84.5 15.0

LW188 G121.0 40.1 164.3 84.2 23.1 60.6 6.7 21.0 121.0 130.0 16.6 119.7 66.9 5.8 46.2 3.2 17.0 138.0 90.9 82.5 15.0

LW142 E

Mean performances of 19 promising ILs under cold water stress and

normal conditions in 2009 and 2010 (Meng et al. 2012)

LW142 E136.7 39.3 162.7 79.2 21.5 57.7 6.7 23.9 112.0 121.5 16.7 119.8 61.6 5.2 43.1 3.2 18.1 134.0 91.2 60.0 15.0

LW154 E137.8 39.9 198.3 82.9 21.9 58.0 5.4 23.4 112.0 128.5 19.7 160.7 67.4 7.4 47.7 3.0 17.4 130.0 121.6 71.3 15.0

LW174 F129.5 37.6 151.3 86.6 21.7 61.0 6.7 25.9 115.0 120.3 17.7 122.0 48.2 5.3 41.4 4.2 17.8 128.0 126.2 80.3 25.0

LW207 G132.6 40.0 192.8 79.9 22.1 58.0 5.8 21.2 121.0 127.0 20.1 118.3 66.6 6.7 43.1 3.8 17.5 132.0 115.1 83.7 20.0

LW264I

138.8 40.7 221.5 77.7 22.6 58.0 5.3 24.9 107.0 130.0 17.2 169.2 26.3 3.1 29.1 2.8 17.9 125.0 120.3 79.1 42.5

LW250 I130.7 39.2 226.8 79.9 23.3 62.6 5.2 26.0 110.0 136.8 20.1 136.8 65.1 5.8 38.4 2.7 18.0 132.0 108.4 76.1 20.0

LW156 E138.9 40.3 187.8 78.9 21.0 55.0 5.7 23.0 114.0 127.0 20.2 129.7 57.9 6.8 43.0 4.0 16.3 129.0 131.8 74.0 15.0

LW151E

131.9 37.7 168.3 82.9 19.2 53.9 5.6 24.2 114.0 122.3 19.3 123.5 67.2 6.6 43.3 3.3 16.6 130.0 122.4 82.9 16.3

LW189 G132.4 37.9 198.3 84.4 20.1 55.9 4.8 21.7 120.0 133.2 19.0 114.7 59.5 6.2 41.1 3.5 17.0 137.0 103.4 75.7 20.0

LW216G

129.1 37.3 170.8 87.1 20.1 56.9 5.4 20.7 123.0 111.8 17.1 99.8 51.7 4.3 34.4 2.8 15.9 139.0 99.9 86.1 16.9

LW200G

127.7 38.6 167.8 88.8 20.5 56.1 5.6 20.3 115.0 122.0 16.4 100.2 66.2 4.9 41.9 3.3 16.5 130.0 93.7 84.2 17.5

LW291I

121.1 33.1 181.5 84.8 17.5 56.5 4.7 25.1 120.0 126.3 24.9 156.3 39.1 6.6 32.2 4.2 17.7 131.0 143.6 74.5 45.0

LSD0.05 1.9 2.1 8.2 2.6 1.6 1.8 0.3 0.5 1.9 3.7 1.8 11.1 8.1 1.2 4.3 0.4 1.1 1.6 8.2 6.2 4.5

The hidden diversity for highly

heritable traits – BLB resistance

P1 P2 P3b P3c P4 P5 P6 P7 P8 P9a P10 P9c P9b P9d

PXO

61

PXO

86

PXO

79

PXO

340

PXO

71

PXO

112

PXO

99

PXO

145

PXO

280

PXO

339

PXO

341

PXO

347

PXO

349

PXO

363

aver

age

HHZ 9.8 21.2 13.1 25.7 10.4 2.4 29.6 5.0 8.6 28.8 8.4 26.6 15.2 24.6 16.4

Reactions (lesion lengths) of HHZ and two donors to 14

tropical races of BLB caused by Xanthomonas oryzae pv oryzae

HHZ 9.8 21.2 13.1 25.7 10.4 2.4 29.6 5.0 8.6 28.8 8.4 26.6 15.2 24.6 16.4

PSBRC66 6.4 18.5 16.4 21.4 11.6 0.7 13.0 2.6 8.8 4.1 7.0 12.0 3.4 17.3 10.2

PSBRC28 2.8 20.3 21.6 24.0 11.2 3.9 22.4 4.7 9.2 26.0 8.5 23.7 22.9 21.9 15.9

8个黄华占群体对15个Xoo菌株产生反应类型（2012年8月，北京）

对全部15个小种高抗的株系对全部15个小种感病的株系对部分小种抗病的株系

F1F1F1F1----F5F5F5F5 F6F6F6F6----F10F10F10F10 F11F11F11F11----F15F15F15F15 F1F1F1F1----F5F5F5F5 F6F6F6F6----F10F10F10F10 F11F11F11F11----F15F15F15F15 F1F1F1F1----F5F5F5F5 F6F6F6F6----F10F10F10F10 F11F11F11F11----F15F15F15F15

Blast evaluation of virulent strainsBlast evaluation of virulent strains Evaluation of BB resistance of >500 Evaluation of BB resistance of >500

lines (HHZ background) against 14 lines (HHZ background) against 14

strains of 10 strains of 10 XooXoo races, 2010 WSraces, 2010 WS

HHZ is

susceptible to

most tropic

BLB races

Vera Cruz et al

PX

O61

PX

O86

PX

O79

PX

O34

0

PX

O71

PX

O11

2

PX

O99

PX

O14

5

PX

O28

0

PX

O33

9

PX

O34

1

PX

O34

7

PX

O34

9

PX

O36

3

aver

age

HHZ 9.8 21.2 13.1 25.7 10.4 2.4 29.6 5.0 8.6 28.8 8.4 26.6 15.2 24.6 16.4

PSBRC66 6.4 18.5 16.4 21.4 11.6 0.7 13.0 2.6 8.8 4.1 7.0 12.0 3.4 17.3 10.2

HHZ15-SAL13-Y2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ15-SAL-13-Y3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ15-DT7-SAL1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

Ten HHZ ILs with broad spectrum resistance to all 14 races

of bacterial blight pathogen, Xanthomonas oryzae pv oryzae

HHZ15-DT7-SAL1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ15-DT7-SAL3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ15-DT7-SAL6 0.2 0.2 0.2 0.2 9.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.9

PSBRC28 2.8 20.3 21.6 24.0 11.2 3.9 22.4 4.7 9.2 26.0 8.5 23.7 22.9 21.9 15.9

HHZ19-SAL-14-Y3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ19-DT8-SAL2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2

HHZ19-SAL12-

SAL4 0.2 0.7 0.9 0.5 0.2 0.2 0.2 0.2 0.4 0.2 0.3 0.9 0.2 0.2 0.4

HHZ19-SAL14-

SAL4 0.2 1.0 0.6 0.3 0.2 0.2 0.2 0.2 0.3 0.2 0.7 0.2 0.2 0.2 0.3

HHZ19-SAL15-

SAL2 0.2 3.8 2.2 0.6 0.4 0.4 0.8 0.5 0.3 0.3 0.3 0.6 0.4 0.4 0.8

Race R% (LL <3.0 cm)

P1 76.4

P2 4.7

P3b 4.9

P3c 4.9

P4 22.4

P5 78.4

Reactions of 512 HHZ ILs to 14 tropical Xoo races

P5 78.4

P6 5.1

P7 46.6

P8 31.0

P9a 12.3

P10 12.1

P9c 4.7

P9b 5.1

P9d 50.8

P10

P8

P7

P4

P5

P1

Xooraces

Classification of 14 Xoo races into two major groups (virulent

and less virulent ones) based on the reactions of the 512 HHZ ILs

Weak virulence group

Average Distance Between Clusters

P9b

P9a

P3b

P3c

P6

P9c

P2

0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3

Name Xoo

High virulence group

Name of lines

H12-33H12-12H9-63H11-27H8-45H19-9H12-15H12-7H12-4H12-9H11-24H12-48H11-55H11-11H19-35H12-36H11-54H8-54H5-60H12-31H15-11H8-18H5-55H15-30H9-4H17-53H19-56H15-24H12-54H15-25H15-8H19-36H19-59H9-66H19-50H19-57H15-21H12-64H15-19H17-5H12-55H12-61H12-40H11-50H8-38H9-9H17-34H19-14H11-16H9-51H19-29H12-18H19-46H12-20H9-41H12-24H19-15H11-31H19-13H19-55H17-35H15-43H9-70H11-28H12-2H19-45H12-39H11-49H11-45H11-34H11-36H11-30H11-32H12-16H8-55H9-40H12-26H11-10H17-32H5-26H19-23H19-22H9-56H19-18H12-17H8-26H8-40H9-18H8-41H5-6H9-25H9-14H8-47H5-59H8-31H8-21H5-51H9-24H15-26H5-5H8-33H12-27H17-11H19-48H8-3H5-13H5-12H9-26H9-16H8-51H8-13H9-7H8-23H8-8H15-1H5-49H17-29H15-12H8-44H5-32H9-13H9-3H17-65H9-20H8-27H5-1H9-39

Classification of the 512 ILs based on their resistances to the 14 Xoo Phillipines racesName of lines

Average Distance Between Clusters

H19-62H19-58H15-38H15-42H15-40H19-19H15-35H9-23H15-13H19-5H12-58H8-36H8-34H5-65H8-6H5-43H17-18H15-32H5-39H17-40H5-15H9-32H11-23H5-72H5-63H8-30H5-10H9-17H5-42H8-22H5-52H5-28H17-36H15-33H5-53H5-48H17-66H17-68H5-67H5-66H17-60H5-61H15-9H15-6H8-39H5-35H5-36H8-28H9-12H5-23H5-3H15-44H17-45H17-28H17-57H9-38H17-62H17-48H17-39H17-52H17-49H17-21H17-13H17-24H17-14H17-19H17-9H11-38H9-22H11-40H11-37H5-41H8-35H8-15H17-63H5-54H9-21H9-19H8-53H5-33H19-16H12-14H8-7H19-47H12-49H11-5H8-12H19-1H5-29H17-64H12-45H8-46H9-15H8-50H17-38H5-21H5-18H5-74H5-11H12-29H11-19H11-17H5-75H12-5H8-52H17-1H15-31H12-65H12-28H8-42H8-10H19-4H12-13H19-7H11-25H9-6H11-21H9-37H17-54H11-33H12-42H12-33H12-12H9-63H11-27H8-45

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

Are the parental performances

correlated with the performances

of their BC progenies?

Genetic background effects in

introgression breeding

VG Donors TKM9 (SS)

(I)

Khazar (SS)

(I)

FR13A (T)

(J)

I IR64 (S) 12 8 14

TotalOrigin

India 34

Number of submergence tolerant plants in 9 BC2F2and 3 BC3F2 populations under the field condition

Submergence Tolerance

I Teqing (SS) 10 9 8

Total

NPT (SS)

BC2F2J

India

Iran

27

6 18

38 94 30 162

6 6

NPT (SS)

BC3F2J Iran 10 8371 2

15

20

25

Yield responses of the 193 parental lines of IRMBP

to the terminal drought under the lowland condition

-19.1±±±±44.0%

0

5

10

15

-100 -80 -60 -40 -20 0 20 40 60 80 100 120 140 160

Yield reduction (in %)




NPT IR64 Teqing

897 2775 489

Total

4161

# of selected plants

per population

8.5

(3.8%)

22.4

(10.0%)

6.3

(3.0%)

13.2

(6.8%)

Range

No. of I donors

0 - 85 0 - 100 0 - 30 0 - 100

59 67 59 185

per population (3.8%) (10.0%) (3.0%) (6.8%)

No. of J donors 32 45 19 96

No. of populations 113 124 105 320

Contributing donors (%) 80.5 90.3 74.3 87.8

Parental performance and 442 selected DT BC2F2plants for drought tolerance from 19 BC populations

VG Donors IR64 (S) Teqing (M) NPT(SS)

I BR24 (MR) 14 (27) 12 (7) 3

I STYH (S) 20 (26) 4

I OM1723 (S) 7 (17) 7 (6) 0

TotalOrigin

Bangladesh

Myanmar

Vietnam

29 (34)

LL (UL) LL (UL) LL

24 (26)

14 (23)

-

J FR13A (SS) 15 (16) 17 (15) 0

J Type3 (S) 23 (15) 10 (12) 0

J Binam (M) 20 (19) 14 (13) 1

J HAN (M) 11 (13) - 3

Zihui100 (S) 8 - 9I

Total

Khazar (MR)J

India

India

Iran

China

China

Iran

32 (31)

33 (27)

35 (32)

14 (13)

58 58

17

176 (133) 60 (53) 22 256 (186)

-

Comparison of different IR64 and NPT BC generations

in screening for anaerobic germination (%)

BC2F2 bulks BC3F2 bulks BC4F2 bulks

IR64 NPT IR64 NPT IR64 NPT

Total number of populations 9 10 - 10 9 10

Surviving plants/population 0 – 28 0 - 50 - 33 - 78 17 - 78 97 - 162

Number of indica donors 7 8 - 8 7 8Number of indica donors 7 8 - 8 7 8

Selected lines (indica) 36 158 - 452 296 1038

Selection intensity (%) 5.1 19.8 - 28.3 21.1 64.9

Number of japonica donors 2 2 - 2 2 2

Selected lines (japonica) 2 8 - 35 44 121

Selection intensity (%) 2.0 8.0 - 17.5 22.0 60.5

Mean selection intensity (%) 4.4 13.9 26.1 21.3 62.7

BC2F2, BC3F2 and BC4F2 bulks all had 200 seeds in 2 replications. For individual BC populations of

200 plants, a difference of 4% between two populations in selection intensity (survival rate) is

statistically significant at P < 0.05 when the selection intensity is between 0.1 and 0.5.

Screening for seedling cold tolerance

Twelve-day old seedlings were subjected to cold temperature for

18 days at the mean daily temperature of 11.8 Co, including 3-day

of low temperature at 8 Co between April 24-26 (LAAS, 2002).

Selection of 861 C418 plants with seedling cold tolerance

from 28 C418 BC2F2 populations 2002 (LAAS)

# of populations 28 2 26

BC2F2 CT donorsNon-CT

donors

Seedling Cold Tolerance (from NARES)

Range 1.4 – 19.3%

# of surviving plants

per population10.3%

The mean population size was 310, ranging from 196 – 465, the

recipient, C418 (japonica) was killed by the stress.

10 – 16% 0 – 3.0%

0.314%

# of surviving plants

per BC population10.3% 10.5%7.6%

Genetic background effects on the

performance of BC progenies

Teqing / Chipda NPT / Chipda

Donor Recurrent parent Donor Recurrent parent

ASD 16 10*** 0 Moroberekan 13 11

ASD18 59*** 0 54*** MR 77 31**** 0

B4122 37*** 2 1 Palung 2 33 36

Budda 75*** 11 Pokhreli 119**** 7 30***

IR64 Teqing NPT IR64 Teqing NPT

Donor and recipient effects on the number of BC2F2 plants

selected under lowland drought during the 2002 dry season

Budda 75*** 11 Pokhreli 119**** 7 30***

Chipda 47*** 0 85**** Pusa 15** 4

Chorofa 1 20*** Rasi 63*** 9

Dacca 6 20 19 Rusty Late 38**** 2 4

Dhan4 1 0 Sadajira 19 55**** 0

Doddi 81*** 2 Shwewartun 5* 0 6**

Gajale 61*** 22 SLG-1 26**** 0

Giza 14 29*** 4 SML242 6** 0 5*

IR64/SN89366 3.33 1.87 NPT/C418 0.00

Teqing/SN89366 6.67 3.75 IR64/CH448 9.33 4.14

NPT/SN89366 0.00 Teqing/CH448 7.33 3.25

IR64/Y134 7.33 3.45 NPT/CH448 0.00

Teqing/Y134 7.33 3.45 IR64/FR13A 7.67 3.64

NPT/Y134 0.00 Teqing/FR13A 6.67 3.17

IR64/BR24 8.00 3.61 NPT/FR13A 0.00

Cross Survival (%) Zvalue Cross Survival(%) Z value

Genetic background effects on the number of survival plants under submergence

in 33 BC4F2 populations from crosses between 3 RPs and 11 donors

Teqing/BR24 8.00 3.61 IR64/Madhukar 7.33 3.60

NPT/BR24 0.00 Teqing/Madhukar 6.00 2.95

IR64/Zihui 100 11.67 4.87 NPT/Madhukar 0.00

Teqing/Zihui 100 7.33 3.06 IR64/IR50 6.67 3.13

NPT/Zihui 100 0.00 Teqing/IR50 8.00 3.76

IR64/IR72 8.00 0.45 NPT/IR50 0.00

Teqing/IR72 8.00 0.45 IR64/Jhona349 5.00 2.73

NPT/IR72 7.00 Teqing/Jhona349 5.67 3.09

IR64/C418 7.33 3.19 NPT/Jhona349 0.00

Teqing/C418 10.00 4.35

Can we develop ILs with extreme

phenotypes for selected target

traits?

Selection for cold tolerance at the booting stageSelection for heat tolerance at the flowering stage

Seed set (%)Seed set (%) Spikelets per panicle

Donor 1N SI (%) 2

Mean 3 RangeN SI (%)

Mean 3 Range Mean 3 Range

Bg90-2 (I)41 9.11 63.3 d 50.3 - 86.5

25 6.25 41.3 abc 23.0–77.0 171.2 abc 124.0–253.1

X21 (I) 29 6.44 64.3 cd 50.6 - 87.19 2.25 38.1 abcd 19.5–50.0 192.5 ab 143.3–275.5

X22 (I) 28 6.22 65.6 bcd 50.7 - 87.3- - - - - -

Q5 (I) 31 6.89 71.1 abc 50.9 - 91.46 1.50 41.1 abc 19.9–75.4 160.4–274.2

Screening results of 11 BC2F4 backcross populations derived from crosses between a

japonica variety, Chaoyou 1 (the recurrent parent) and 11 donors for cold tolerance at the

booting stage and for heat tolerance at the flowering stage

Q5 (I) 31 6.89 71.1 abc 50.9 - 91.46 1.50 41.1 abc 19.9–75.4 160.4–274.2

Chhomrong (J) 24 5.33 51.4 - 87.817 4.25 37.7 abcd 19.3–65.5 172.9 abc 115.9–258.8

Doddi (I) 25 5.56 71.0 abc 50.2 - 90.0- - - - - -

Feng-Ai-Zhan (I) 44 9.78 52.2 - 98.512 3.00 31.3–70.1 180.7 abc 138.2–238.0

Shennong265 (J) 21 4.67 69.2 abcd 50.7 - 93.89 2.25 28.9 d 17.0–44.4 171.5 abc 112.0–216.7

Yuangeng7 (J) 41 9.11 71.1 abc 50.0 - 90.125 6.25 45.5 ab 23.9–65.6 83.2–255.4

OM997 (I) 21 4.67 72.1 ab 54.9 - 89.613 3.25 33.0 cd 17.0–48.9 171.9 abc 111.6–230.4

Cs94 (I) 19 4.22 64.2 cd 51.4 - 86.08 2.00 33.6 abcd 24.9–48.3 175.5 abc 121.4–280.4

Chaoyou (J) 324 6.55 24.8 e 19.0 - 30.0124 3.44

5.2 e 0.0–7.9 157.4 bc 127.4–178.6

2 N is the number of cold tolerant or heat tolerant BC plants selected from each population and SI = selection intensity.3 Different letters indicate the statistical significance in seed set at P < 0.05, based on the Duncan testing of ANOVA.

Table 6 Performances for AG of 11 promising BC4F3 lines and their donors

Recipient Donor Seedling height (cm) AG (%) Emerging at 10 d (%)

NPT Khazar 33.5 90.0* 20.0

NPT Khazar 32.5 95.0** 75.0**

NPT FR13A 37.7 95.0** 30.0

NPT TKM 9 37.7 100.0*** 95.0***

NPT TKM 9 36.2 100.0*** 60.0*

NPT TKM 9 37.9 100.0*** 95.0***

NPT Babaomi 34.9 100.0*** 50.0

NPT Babaomi 36.7 100.0*** 50.0

NPT OM1706 33.9 100.0*** 65.0*

NPT OM1706 36.1 100.0*** 80.0***

TKM 9 I 31.4 20.0 12.7

Khazar J 30.3 3.0 0.0

Babaomi I 26.3 5.0 0.0

Jiangxi-Si-Miao I 31.5 9.0 0.0

OM1706 I 29.1 18.0 2.0

IR64 I 26.5 20.0 2.0

NPT J 36.2 68.0 39.0

I = indica and J = japonica. Traits were measured at 21 d after seeding. All 10 ILs had significantly higher AG than the

recurrent parent, NPT at P < 0.001.

Drought tolerance 350 4687

BPH resistance 203 522

Salinity tolerance 203 1022

Target traits# of BC2F2populations

No. of selected

BC2F3 lines

Trait specific introgression lines developed

Anaerobic germination 130 368

Zinc deficiency 129 1211

Submergence tolerance 264 798

Grain quality 65 580

Other traits 375 12,000+

Total 20,000+

Summary of Selection Experiments

• Most donors contributed performance enhancing

alleles to their BC progenies regardless of their

performances;

• Appropriate screening (selection) is the key to

identify improved target traits in the BC identify improved target traits in the BC

progenies;

• More distantly related donors, particularly

landraces, tend to give more transgressive

segregations for abiotic tolerance in the BC

progenies.

� There are tremendous amounts of hidden genetic

diversity in the current rice germplasm

collections for genetic improvement of all target

traits we tried, which have not been exploited;

� Selection of parental lines for breeding based on

Conclusions

� Selection of parental lines for breeding based on

phenotype practiced by most breeders is a poor

way in exploiting novel genetic variation for

complex traits;

� Backcross breeding, effective selection (efficient

screening) combined with DNA markers are the

effective way to exploit this hidden diversity;

What are we going to do with

this large number of ILs?

1. Direct development of new cultivars;

2. As genetic stocks for discovery of DT alleles 2. As genetic stocks for discovery of DT alleles

or QTLs and functional genomics of DT;

3. As parents for development of superior rice

cultivars by QTL pyramiding

Progeny Testing of DT ILs Under Stress

(no irrigation after transplanting)

Check (C418)DT C418 ILs

Progeny Testing Under Stress

(no irrigation after transplanting)

Promising DT C418 ILs

2001-2002 DS BC2F4 progeny testing

IR64 (CK) DT IR64 ILsIR64 ILs for quality

Performance of two DT NPT ILs under severe stress

DT NPT ILs NPT CK

Performance of some promising salinity

tolerant IR64 ILs in the field condition in Iloilo

(EC 18 dSm-1 )

11/17, 2003

Performance of some promising salinity

tolerant IR64 ILs in the field condition in

Iloilo (EC 18 dSm-1 )

11/17, 2003

Promising varieties

developed in the BC

breeding programbreeding program

The Recurrent Parents

C418

(restorer)Liaojing454

Preliminary Yield Trials of Promising

DT/WUE ILs

30%

water

saving

70%

water

saving

50%

water

saving

Replicated Preliminary yield trial of DT/WUE ILs

(Shengyang/2006.9)

Completely

rainfed

Water

saving

70%

Water

saving

50%

Water

saving

30%

Promising DT/WUE

IL -HR95辽粳辽粳辽粳辽粳9号对照号对照号对照号对照

抗旱导入系的节水实验抗旱导入系的节水实验抗旱导入系的节水实验抗旱导入系的节水实验

30% water saving

10

15

20

25

Normal irrigation

Yield change over CK (%)

Yield performances of two promising DT/WUE

ILs in replicated yield trials under stress and

non-stress conditions (Shengyang/2006)

Completely rainfed

70% water saving

50% water saving

-5

0

5

10

HR94 HR95 Liaojing 9

(CK)

Yield change over CK (%)

in Liaojing 454background

10

15

20

25

Rainfed 70% 50% 30% Normal% change over CK

Yield potential and DT/WUE of DT ILs

-10

-5

0

5

10

HR354

(C418)

HR525

(C418)

HR9

(C418)

HR94

(LJ454)

HR95

(LJ454)

LJ9

(CK)

Promising DT/WUE FAZ ILs

Zhonghua 2Zhonghua 1

GSR material ST in Infanta

• GSR material

• material (572 lines)• material (572 lines)

• Other group’s material

2011-10-20

Lijun Meng

s

High EC Low EC

GS

R

NON-

GSRs

e

a

R GSR

NON GSR material

GSR material

HHZ HHZ HHZ HHZ 23-Sal8-DT1-ST1

HHZ 23-Sal24-DT1-STI HHZ 23-Sal8-DT1-ST1 HHZ 22-DT3-LI1-DT1HHZ 23-Sal24-DT1-STI

R1 R2

CK

NSIC Rc 222

2011-10-7

HHZ 24-DT6-DT1-

DT1

HHZ 23-DT14-DT1-DT1IR 63307-4B-4-3

2011-10-7

HHZ 25-SAL9-Y3-ST1

Introgression Breeding for

improving 2 or more

complex traitscomplex traits

RP DonorsX

BC2F1

BC2F2

X

Screening under

severe drought

Selection for high yield

under normal condition

Screening under

severe salinity

Screening under

submergence

Promising ILs with more than one target traits to be

tested in multi-location yield trials in target Es

DT ILsST ILs HY ILsSUBT ILs

PT under severe

drought

PT for high yield under

normal condition

PT under severe

salinity

PT under

submergence

An example of the modified

introgression breeding procedure

used in GSR development

--

Development of HHZ ILs with one or

more improved target traits (yield, DT, ST,

SUBT and performance under low inputs)

Huang-Hua-Zhan (HHZ) is a mega rice variety

with high yield potential, superior quality

currently grown in ~2 million ha in South and

central China. It has wide adaptability (yielded

significantly higher than the best local checks) at

> 17 testing sites of Asia and Africa

Cote D’ivoir

Mali

Rwanda

Nigeria

Mozambique

Tanzania

Bangladesh

Indonesia

Pakista

n

Vietnam

Philip

pines

All

HHZ 2 1 3 1 3 1 2 1 1 1 1 17

Two batches of 16 populations with HHZ as the recipient and

16 donors from 9 different countries

Batch Pop. Donor Country of origin Gen.(10 DS)

1 HHZ5 OM1723 Vietnam (I) BC1F5

1 HHZ8 Phalguna India (I) BC1F5

1 HHZ9 IR50 IRRI (I) BC1F5

1 HHZ11 IR64 IRRI (I) BC1F5

1 HHZ12 Teqing China (I) BC1F5

1 HHZ15 PSB Rc66 Philippines (I) BC1F5

1 HHZ17 CDR22 India (I) BC1F51 HHZ17 CDR22 India (I) BC1F5

1 HHZ19 PSB Rc28 Philippines (I) BC1F5

2 HHZ1 Yue-Xiang-Zhan China (I) BC1F4

2 HHZ2 Khazar Iran (J) BC1F4

2 HHZ3 OM1706 Vietnam (I) BC1F4

2 HHZ6 IRAT352 CIAT (upland) BC1F4

2 HHZ10 Zhong 413 China (I) BC1F4

2 HHZ14 R644 China (I) BC1F4

2 HHZ16 IR58025B IRRI (I) BC1F4

2 HHZ18 Bg304 Sri Lanka (I) BC1F4

The Introgression Breeding Procedure

First batch of 8 HHZ BC1F2 populations (08WS)

DT screen SUB screen

3 SUBT plants

311 genotyped/progeny tested for all target traits

Random plants

109 DT plants

Yield traits

QTL/Allelic

diversity

discovery

for target

82 HY plants

ST screen

120 ST plants

06WS

08WS

09DS

1st round selection

12 RYT and 108 PYT under DT, low input, NC

Confirming genetic

networks for target

traits and their

genetic relationships

for target

traits

68 promising ILs

153 DT screen 171 SUB screen212 Yield 211 ST screen09DS

09WS 495 genotyped/progeny tested for all target traits

10DS

10WS/11DS68 replicated

yield trials

Used as parents for

designed QTL

pyramiding2 NCT

in 11WS3 Demo

2nd round selection

3rd round selection

The Introgression Breeding Procedure

Second batch of 8 HHZ BC1F2 populations (09WS)

DT screen SUB screen

21 SUBT plants

664 genotyped/progeny tested for all target traits

Random plants

210 DT plants

Yield traits

QTL/Allelic

diversity

discovery

for target

traits

119 HY plants

ST screen

314 ST plants

DT screen SUB screenYield under

NC & LIST screen

06WS

08WS

10DS

Confirming genetic

networks for target

traits and their

genetic relationships

traitsNC & LI

176 DT ILs 221 SUB ILs491 HY&FUE ILs 44 ST ILs

10WS 865 genotyped/progeny tested for all target traits

11DS

Promising ILs as parents for

designed QTL pyramiding

130 DT screen SUB screen232 yield

under NC&LIST screen

570 DT ILs SUB ILs305 HY&FUE ILs ST ILs

PYT11WSRYT &

DEMO

HHZ ILs with one or more improved target traits selected

from the 8 2nd BC populations

Improved traits Selected

ILs PYT NCYT

DT+LI 210 24 8

DT+ST 58 13 5

DT+SUBT 24 14

DT+HY 28 28 16

LI+ST 0 0 1

LI+HY 25 2

ST+SUBT 1 9ST+SUBT 1 9

ST+HY 33 33 8

SUBT+HY 7 2 1

DT+ST+SUBT 35 3 1

DT+ST+HY 154 9

DT+SUBT+HY 58 3

LI+ST+SUBT 20

LI+ST+HY 117

LI+SUBT+HY 36

ST+SUBT+HY 39

Total 845 140 40

Traits InstitutionNumber of

donorsILs selected

Drought toleranceCAAS

IRRI

8

15

180

978

CAAS 40 1200

Trait specific HHZ ILs developed in

CAAS and IRRI in 4 years

Salt toleranceCAAS

IRRI

40

15

1200

633

Tolerance to low inputs IRRI 250 350

Submergence tolerance IRRI 4 121

High yieldCAAS

IRRI

8

15

210

610

High yield under low

inputsIRRI 451 451

TotalCAAS

IRRI

40

15

1809

1260

Designation

Grain Yield (t/ha)Mean

over

seasons

% over

IR72

% over

NSICRc1

582010WS 2011DS

HHZ8-SAL6-SAL3-Y2 6.55ab 8.0ab 7.28 10.56 12.27

Performances of some high yield HHZ

ILs under irrigated conditions at IRRI

Mestizo7 (Hybrid) 5.68 bcde 8.7a 7.19 9.27 10.96

HHZ12-DT10-SAL1-DT1 6.75a 7.2 bcde 6.98 6.00 7.64

HHZ5-SAL10-DT1-DT1 6.14abcd 7.4 bcd 6.77 2.89 4.48

IR72 5.96abcde 7.2 cde 6.58 0.00 1.54

NSICRc158 5.86 bcde 7.1 cdef 6.48 -1.52 0.00

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

Plot size: 30 sqm under SSNM

DT HHZ5-Sal14-Sal2-Y2 APO (check)

3000

4000

5000

6000

Viscosity, cP

60

80

100

120

Temperature

1 2

3 4

5 6

7 8

9 10

11 12

13 14

15 16

17 18

The HHZ ILs in RYT have diverse grain pasting properties

suitable for consumers with different taste preferences

-1000

0

1000

2000

0 100 200 300 400 500 600 700 800

Time, sec

Viscosity, cP

0

20

40

60

Temperature

17 18

19 20

21 22

23 24

25 26

27 28

29 30

31 32

33 34

35 36

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

BC2F2Bulk populations

Drought screen – DT ILsScreen for the

primary target trait

SalinityDisease and

insect resistances

Screen for

other traitsYield related

traits

QTL & QTL

networks for

Genotyping

Development of ILs with resistances to multiple

abiotic/biotic stresses

insect resistancestraits networks for

target and non-

target traits

Promising ILs with multiple

desirable traits (QTLs)

Parents for DQP Promising lines

Breeding by

DQP procedures

Yield trials at

multiple locations

IR# RP(%) Donor BPHR

(Score)

SBR

(LL, cm)

ST

(Score)

SUB

(%)

Yield/plant (g)

Mean CK%

IR82853-18 84.4 Type 3 3.2 3.0 25.7 68.6

IR82853-30 84.2 Type 3 3.0 3.8 27.2 77.9

IR82908-5 75.8 Bg300 3.0 4.0 17.9 17.1

IR82907-18 89.1 Babaomi 3.0 3.7 - -

IR82855-26 81.0 Binam 3.0 4.0 26.7 74.8

IR82861-10 80.5 RF13A 3.0 4.0 17.4 13.6

Development of IR64 ILs with multiple desirable traits

IR82861-10 80.5 RF13A 3.0 4.0 17.4 13.6

IR82865-2 89.5 Haonnong 3.0 3.0 15.9 3.9

IR82859-24 88.6 OM1723 3.0 4.0 20.7 35.3

IR82940-7 84.3 Basmati 3.0 100.0 - -

IR82863-2 79.5 Zihui 100 3.0 100.0 26.0 70.3

IR82855-1 91.7 Binam 3.0 3.0 22.1 44.7

IR82859-13 97.1 OM 1723 3.6 4.0 17.7 15.8

IR82865-24 89.5 Haonnong 3.0 4.0 88.9 34.5 125.8

IR82861-28 81.4 FR13A 3.0 4.0 100.0 - -

IR64(CK) 100.0 15.3 -

• When we are trying to improve

more than one complex trait, what

Question:

more than one complex trait, what

trait(s) should be selected first,

yield or abiotic/biotic stresses?

1: ST (57)

2: ST (49)

3: ST (56)

1: HY (26)

2: HY (28)

3: HY (29)

HHZ x Donors (1=IR64 , 2=AT354 , 3=C418)

F1 x HHZ

25 BC1F1 x HHZ

25 BC2F1

3 bulk BC2F2s (480)

X

1: DT (19)

2: DT (29)

3: DT (33)1st selection BC2F3s

2010 Beijing Summer

Population

development and

selection

2st selection1: DT (12)

2: DT (23)

3: DT (8)

3nd selection

3: ST (56)3: HY (29)

1: DT (0)

2: DT (0)

3: DT (1)

1: HY (2)

2: HY (1)

3: HY (2)

1: DT (0)

2: DT (0)

3: DT (2)

1: HY (0)

2: HY (2)

3: HY (1)

1: ST (25)

2: ST (28)

3: ST (29)

1: DT (3)

2: DT (4)

3: DT (2)

1: HY (3)

2: HY (5)

3: HY (2)

3: DT (33)1 selection

BC2F4s

BC2F5s

1: HY (0)

2: HY (2)

3: HY (3)

2010 Beijing Summer 2010 Hainan Winter 2010 Winter phytotron

2010 Hainan Winter 2010 Hainan Winter

Donor 1N T HD PH FGN TGW SNP SF PN GY

HHZ

(RP)

N Mean116.2±3.2 75.6±1.4

23.4±0.6 175.4±16.1 192.0±18.3 90.7±1.8 8.3±1.2 22.0±1.3

S Mean107.3±11.5 74..0±1.6

21.0±0.4 137.1±13.7 154.4±14.2 86.4±2.0 8.8±1.2 17.6±0.7

IR64 26

N

Mean111.8±5.1 75.6±4.4

22.5±3.0 171.9±47.6 197.3±49.3 86.8±5.5 7.9±1.6 22.7±6.6

Range101.0-111.0 66.3-78.9

15.2-26.0 106.7-255.8 136.3-272.4 74.4-93.8 6.2-10.6 12.8-32.6

S

Mean91.3±5.2 71.3±4.7

20.2±1.8 135.1±31.8 154.3±30.2 74.3±11.2 9.2±2.3 14.8±±±±5.2

Range78.0-99.5 65.0-77. 5

17.5-22.6 80.2-194. 9 98.1-203.6 49.4-91. 4.4-14.3 4.3-23.9

Performances of 83 HHZ BC2F5 introgression lines selected for high yield and their RP (HHZ)

under drought stress (S) and normal (N) conditions of Hainan in 2010 (1N: number of HY ILs, T:

treatment, N: normal condition, S: drought stress condition,)

78.0-99.5 65.0-77. 5

AT354 28

N

Mean107.1±7.3 72.5±2.3

20.3±1.0 184.8±28.8 231.0±31.4 79.9±4.3 10.2±1.6 27.6±5.5

Range98.5-110 69.2-74.8

19.0-22.0 127.8-217.8 166.7-273. 1 72.7-85.7 8.7-12.3 19.3-35.0

S

Mean90.1±7.0 65.7±3.9

18.6±1.2 119.1±19.7 145.3±26.4 63.3±13.4 9.6±1.9 10.9±±±±3.6

Range82.0-99.0 58.5-68.9

17.1-20.5 73.4-156.1 101.6-176.5 51.1-80.2 7.3-12.5 6.9-19.1

C418 29

N

Mean111.6±4.3 76.2±3.7

23.2±1.7 192.1±36.3 217.2±40.0 88.4±5.3 7.8±1.5 24.4±5.7

Range99.5-117.5 76.4-81.2

20.6-26.1 99.7-228. 7 142.4±270.6 70.4-92.5 4.6-11.7 13.9-40.4

S

Mean97.7±5.7 75.4±5.5

20.8±1.5 143.6±28.8 155.4±24.4 79.2±12.1 9.2±1.6 18.7±5.9

Range86.5-103 69.7-80.4

18.0-23.0 87.1-175.7 114.2-197.3 55.6-89.7 7.2-11.8 7.6-26.5

Donor T N1

HD PH GW FGW SNP SF PN GY

N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2

IR

N

26 0 5 0 2 1 4 1 1 1 0 0 6 0 0 2 0

AT354 16 0 9 0 1 0 12 0 1 1 0 0 12 3 0 1 0

C418 22 0 3 0 0 0 2 0 1 1 0 0 1 1 1 2 0

The numbers of ILs selected for high yield from the 3 populations that deviated

significantly HHZ for 9 measured traits evaluated under drought stress (S) and normal

(N) conditions of Hainan in 2010

C418 22 0 3 0 0 0 2 0 1 1 0 0 1 1 1 2 0

IR

S

26 0 25 2 5 0 5 0 5 0 1 0 6 0 2 0 2

AT354 16 0 16 0 15 0 6 0 9 0 0 0 13 1 0 0 7

C418 22 0 15 2 0 0 1 0 1 0 0 0 1 0 0 1 1

N1 is the total number of selections based on grain yield (GY) per plant in BC2F5 populations. N1 and N2 are the

numbers of the BC2F5 lines showing significantly higher or significantly lower than HHZ for the measured traits.

HD = heading date, PH = plant height, PL = panicle length, GW = 1000-grain weight, FGN = filled grain number

per panicle, SNP = spikelet number per panicle, SF = spikelet fertility, PN = panicle number per plant, GY =

grain yield.

L Donor Line#

Under the normal condition Under the drought stress condition

HD PH TGW FGN SNP SF PN GY HD PHTG

WFGN SNP SF PN GY

BJ

HHZ 115.3 - 23.1 172.8 189.0 91.4 7.6 23.1 - - - - - - - -

AT354

WT111 106.0 - 20.4 227.9 260.4 87.5 9.3 39.2 104.0 - 18.6 135.4 142.5 94.7 4.3 8.8

WT115 107.0 - 20.4 208.4 228.5 91.1 8.3 31.6 109.5 - 19.2 106.1 148.7 71.3 3.0 4.5

WT91 101.0 - 18.9 171.4 210.4 81.5 7.0 23.9 104.0 - 16.1 112.6 132.9 85.0 5.5 5.5

WT97 106.5 22.7 144.2 175.2 82.3 6.7 24.9 110.5 19.6 119.6 152.2 78.5 4.0 6.5

C418

WT183 103.5 - 21.0 251.7 300.7 83.7 8.3 33.5 113.5 - 17.5 123.9 151.2 81.9 5.3 5.9

WT184 107.0 - 20.9 187.7 204.7 91.7 8.3 31.6 113.0 - 17.8 117.6 149.6 78.6 5.3 6.0

WT185 103.5 - 21.8 165.6 189.9 87.2 10.7 32.5 115.5 - 19.2 141.7 159.0 89.1 4.0 8.2

Performances of some promising DT ILs under drought stress and normal

conditions in Beijing and Hainan, 2010

WT180 105.0 - 18.8 215.6 240.6 89.6 8.0 23.9 116.0 - 16.8 127.2 199.5 63.7 5.5 4.4

HN

HHZ 116.2 75.6 23.4 175.4 192 90.7 8.3 22.0 107.3 74 21.0 137.1 154.4 86.4 8.8 17.6

AT354

WT111 105.0 68.0 22.3 162.8 189.4 86.0 7.3 19.5 111.0 65.3 19.3 95.8 140.2 68.6 9.0 14.5

WT115 108.0 73.8 22.0 164 195.3 83.9 8.0 20.6 115.5 75.3 20.2 111.1 155.7 71.310.

416.4

WT91 111.0 80.7 20.9 181.8 232.1 78.3 11.5 38.3 119.5 73.5 17.9 123.4 144.9 85.811.

621.6

WT97 109.0 77.2 21.2 274.3 318.7 86.0 8.5 32.3 114.0 68.1 20.8 104.2 161.0 64.9 9.6 17.9

C418

WT183 114.5 76.5 23.8 133.8 145.0 92.3 6.7 22.5 125.0 74.6 20.8 92.9 111.5 83.2 9.9 23.9

WT184 114.0 74.4 24.7 156.3 176.7 88.5 8.6 29.3 125.0 75.6 20.8 123.6 140.6 89.0 6.8 15.5

WT185 113.0 73.3 24.5 174.6 192.2 91.1 9.8 31.3 121.0 72.8 21.4 119.3 132.3 90.2 9.4 26.9

WT180 115.0 81.2 24.5 188.4 200.8 93.8 8.8 36.2 125.0 85 21.9 150.4 183.6 82.1 8.7 26.9

� The selection order of DT(1) – HY(2) was

more effective than that of HY(1) – DT(2)

to combine both HY and DT;

� This result can not be adequately � This result can not be adequately

explained by the current quantitative

genetics theory. However, it does indicate

that it will make differences to determine

the correct order of target traits to be

selected when multiple complex traits are

to be improved.

What are we going to do with

this large number of ILs?

1. Direct development of new cultivars;

2. As genetic stocks for discovery of DT alleles 2. As genetic stocks for discovery of DT alleles

or QTLs and functional genomics of DT;

3. As parents for development of superior rice

cultivars by QTL pyramiding

Uses of ILs for

pyramiding genes/traits

from 2 or more donors to from 2 or more donors to

develop GSR varieties

IL1(HY, DT) x IL2(HY, DT)

F2

Screen

for DT

Screen

for ST

ST

IL3(HY, ST) x IL4(HY, ST)

Select for

HY and

random

Experimental design for simultaneous improvement of

DT, ST and yield potential by pyramiding

F2

Screen

for DT

Screen

for ST

Select for

HY and

random

DT

PDLs

ST

PDLs

Genotyping and progeny

testing for all target traits

Discovering genetic networks for HY, DT,

ST and their genetic overlap

HY, DT, ST

PDLs (PDL1)

DT

PDLs

ST

PDLs

Genotyping and progeny

testing for all target traits

HY, DT, ST

PDLs (PDL2)

Designed QTL pyramiding based on the genetic and

phenotypic information of parental ILs

IR64/BR24//IR64///IR64

BC2F2

IR64/Binam//IR64///IR64

BC2F2

Screening under drought

DT IR64/BR24 IL DT IR64/Binam ILXGenotyping

and QTL

identification

Genotyping

and QTL

identification identificationidentification

F1

F2

X

Screening under severe drought

Survival plants GenotypingProgeny testing

IL1 F2 IL2

Pyramiding F2 population screened under

severe lowland drought at the reproductive

stage (2002-03 DS)

P1 IL P2 IL F2 population

Cross Line Donor Line Donor Size No. SI (%)

II-1 DGI-74 BR24 DGI-187 Binam 318 90 28.3

II-2 DGI-21 STYH DGI-62 BR24 190 55 28.9

II-3 DGI-76 BR24 DGI-238 OM1723 248 55 22.2

An average of 25% of the progeny of the 9 F2populations survived the severe drought stress

II-4 DGI-21 STYH DGI-60 BR24 137 25 18.2

II-5 DGI-29 STYH DGI-353 Zihui100 154 30 19.5

II-6 DGI-75 BR24 DGI-187 Binam 154 30 19.5

II-7 DGI-142 Type3 DGI-373 HAN 255 70 27.5

II-8 DGI-146 Type3 DGI-353 Zihui100 135 70 51.9

II-9 DGI-150 Type3 DGI-374 HAN 219 30 13.7

Total 1810 455 25.1

Yield performances of 90 (3 major group genotypes)

PLs from pyramiding population 1 in 2004 dry-season

Control Terminal stress

2.0

4.0

6.0

8.0

0.4

0.8

1.2

1.6

2.0

GG1 (X = 109±±±±20, 66%)

GG2 (X = 247±±±±35, 149%)

GG4 (X = 117±±±±18, 70%)

GG3 (X = 140±±±±33, 84%)

GG1 (X = 35±±±±8, 361%)

GG2 (X = 33±±±±12, 344%)

GG4 (X = 34±±±±8, 373%)

GG3 (X = 35±±±±13, 364%)

0 0

0.4

GG1 GG2 GG3GG4 IR64 GG1 GG2 GG3GG4 IR64

IR64 (X=166±±±±10, 100%) IR64 (X=9.7±±±±5, 100%)

Yield

Source DF MS F P > F R2 (%)

Stress 1 824575.5 820.64 0.0001 23.2

Group 5 90892.7 90.46 0.0001 12.8

Group(Line) 83 1778.9 1.77 0.0002 4.1

Stress*Group 5 97151.2 96.69 0.0001 13.7

ANOVA Result for Yield of 2004 Dry Season

Stress*Group 5 97151.2 96.69 0.0001 13.7

Stress*Group(Line) 83 1576.9 1.57 0.0029 3.7

Stress

Group 5 312.9 1.17 0.3255 2.0

Group(Line) 83 374.6 1.4 0.0332 40.0

Control

Group 5 187440.6 113.55 0.0001 62.3

Group(Line) 83 3086.6 1.87 0.0003 17.0

Control Stress

100

200

300

400

500

40

60

80

100

120

140

160

Yield performances of the 4 group genotypes under the rainfed

upland stress and non-stress conditions in 2004 wet-season

0

100

0

20

40

GG1 GG2 GG3 GG4 IR64

GG1 (X=50±±±±22, 1111%)GG2 (X=44±±±±24, 978%)GG4 (X=62±±±±31, 1378%)GG3 (X=55±±±±19, 1222%)

GG1 GG2 GG3 GG4 IR64

GG1 (X=124±±±±20, 51%)GG2 (X=310±±±±34, 129%)GG4 (X=122±±±±44, 51%)GG3 (X=212±±±±37, 88%)IR64 (X=241±±±±27, 100%) IR64 (X=4.5±±±±8, 100%)

ANOVA Results for Yield of 2004 Wet Season

12.6 12.6 12.6 12.6 0.0001174.6174.6174.6174.6259596.4 3Stress*Group

4.1 0.00012.063057.4 83Group(Line)

10.7 10.7 10.7 10.7 0.0001147.8147.8147.8147.8219664.33Group

40.4 40.4 40.4 40.4 0.00011676.01676.01676.01676.02491548.91Stress

R2(%)P > FFMSDFSource

YIELD

21.8 21.8 21.8 21.8 0.00013.525591.6 83Group(Line)

65.3 65.3 65.3 65.3 0.0001292.2292.2292.2292.2464372.9 3Group

Control

36.3 36.3 36.3 36.3 0.05271.341773.4 83Group(Line)

6.9 0.00114.264.264.264.265626.6 3Group

Stress

5.8 0.00012.94307.3 83Stress*Group(Line)

12.6 12.6 12.6 12.6 0.0001174.6174.6174.6174.6259596.4 3Stress*Group

2.0

4.0

6.0

8.0

ControlStress

Yield performance of the 4 group genotypes under

mild stress in 2005 dry-season

GG2 GG4 GG3 CK0

2.0

GG1 GG2 GG4 GG3 CKGG1

GG1 (X=237±±±±58, 149%)GG2 (X=313±±±±46, 197%)GG4 (X=227±±±±47, 143%)GG3 (X=249±±±±50, 157%)IR64 (X=159±±±±40, 100%)

GG1 (X=157±±±±29, 75%)GG2 (X=247±±±±33, 119%)GG4 (X=173±±±±38, 83%)GG3 (X=164±±±±28, 79%)IR64 (X=208±±±±57, 100%)

151%

127%

152%

131%

76%

� Strong selection under severe drought resulted in

a few major group genotypes that have

significantly improved DT, and showed highly

Summarized Results from 1st round

pyramiding breeding

significantly improved DT, and showed highly

significant differences in multiple phenotypes

under the non-stress conditions;

� We have identified a group genotype that have significantly improved yield potential and WUE/DT.

1. Large numbers of loci are involved in DT of rice, and these DT loci appear to be under strong epigenetic control and tend to form complex genetic networks with clear hierarchy;

2. Strong selection under severe drought resulted in a few major group genotypes that have significantly improved DT, and showed highly significant differences in multiple phenotypes under the non-stress conditions;

Summary

non-stress conditions;

3. Group 4 loci were associated with severe yield penalty by 30-50%;

4. Group 5 loci were associated with improved yield potential (faster growth rate and greater sink capacity)

5. We have identified promising rice lines with group genotype (1, 2, 3, and 5) that have significantly improved yield potential and WUE/DT. These lines are being tested in the multi-location yield trials in South/Southeast Asia.

• The overall level of DT in rice appears to depend more

on the combination of QTLs and less on the absolute

number of QTLs that remains to be elucidated; and

Summarized results

• High level of DT at the reproductive stage in rice is not

necessarily associated with a penalty in yield potential

under normal irrigated conditions. Thus, it is possible to

combine high level of DT (at least for DT at the

reproductive stage) and high yield potential.

Selection intensity of the 2nd round pyramiding F2populations

P1 PLs P2 PLs F2

Cross Line Origin Line Origin N Drought SI%

III-1 DK47 II-1 DK109 II-2 420 56 13.3

III-2 DK47 II-1 DK148 II-2 428 60 14.0

III-3 DK47 II-1 DK158 II-2 439 97 22.1

III-4 DK47 II-1 DK356 II-3 413 72 17.4

III-5 DK47 II-1 DK388 II-3 425 49 11.5

II-1 II-2 24 32.0 III-6 DK39 II-1 DK148 II-2 75 24 32.0

III-7 DK39 II-1 DK158 II-2 422 70 16.6

III-8 DK39 II-1 DK356 II-3 269 55 20.4

III-9 DK39 II-1 DK388 II-3 435 20 4.6

III-10 DK65 II-1 DK109 II-2 382 50 13.1

III-11 DK65 II-1 DK148 II-2 305 40 13.1

III-12 DK65 II-1 DK158 II-2 403 51 12.7

III-13 DK65 II-1 DK356 II-3 112 20 17.9

III-14 DK65 II-1 DK388 II-3 220 3 1.4

Total 4748 667 15.0

Selection for HY and DT in 14 2nd DQP F2 populations from

crosses bet. 8 IR64 PDLs each with multiple DT QTLs from 2

donors (05-06 DS, IRRI)

Donor1 Donor2 Donor3 Donor4Non-stress Stress

Pop. size Sel. for yield Pop. size Sel. for DT

STYH BR24 BR24 Binam 127 8 (26.7) 75 24 (6.2)

STYH BR24 BR24 Binam 450 21 (27.2) 422 70 (7.4)

STYH BR24 BR24 OM1723 296 25 (26.4) 269 55 (6.6)

STYH BR24 BR24 OM1723 405 20 (22.3) 435 20 (4.5)

STYH BR24 BR24 Binam 450 30 (30.3) 420 56 (9.9)

STYH BR24 BR24 Binam 435 17 (28.6) 428 60 (12.6)

STYH BR24 BR24 Binam 450 18 (32.0) 439 97 (11.3)

STYH BR24 BR24 OM1723 435 31 (26.2) 413 72 (9.4)

STYH BR24 BR24 OM1723 419 17 (22.0) 425 49 (5.4)

STYH BR24 BR24 Binam 435 14 (30.6) 382 50 (8.2)

STYH BR24 BR24 Binam 241 8 (31.4) 305 40 (7.0)

STYH BR24 BR24 Binam 443 21 (23.5) 403 51 (6.7)

STYH BR24 BR24 OM1723 120 9 (29.3) 112 20 (10.1)

STYH BR24 BR24 OM1723 315 15 (31.0) 220 3 (4.5)

Average 358.6 18.1 (27.7) 339.1 47.6 (7.9)

Field screening of the 2nd round DQP F2populations under severe lowland stress

(2005-2006 dry season)

F2 populationMale

PDL1

Female

PDL2

IR64

F2 population

Parental ILs and IR64

Field screening of the 2nd round DQP F2populations under severe upland stress

(2005-2006 dry season)

IR64DK158DK47

Population

Controlled irrigated condition

Field screening of the 2nd round DQP F2 populations

under severe upland stress (05-06 dry season)

PopulationDK47 DK158 IR64

Lowland stress

DK47 DK109 IR64

Population

Controlled irrigated condition

Field screening of the 2nd round DQP F2 populations

under severe upland stress (05-06 dry season)

DK47 DK109 IR64Population

DK47 DK109 IR64

Lowland stress

Uses of ILs for

molecular recurrent

selection (MRS)

Molecular Recurrent Selection (MARS) Systems for Improving

Multiple Complex Traits for Different Target Environments Based

on Trait-Specific ILs and Dominant CMS (under the way)

Composition of the MRS populations: 50+ ILs/PLs carrying favorable QTL alleles from

different donors plus the DCMS line in the same genetic backgrounds

HHZ MRS population MRS population in a New GB

Bulk harvest seeds

from CMS plants to

be screened for

target traits

Bulk harvest seeds

from CMS plants to

be screened for

target traits

Normal plants

CMS plants

Ovals or boxes of different colors represent different ILs carrying genes/QTLs for different target traits

Bulk harvest seeds

from CMS plants to

be screened for

target traits

Selected plants enter

the progeny testing,

genotyping and next

round of RS

Bulk harvest seeds

from CMS plants to

be screened for

target traits

Selected plants enter

the progeny testing,

genotyping and next

round of RS

On-going MRS in phase II of the GSR project

Each MRS population consisting of many ILs/PLs of the same elite GB

50% fertile plants

Flood prone

Rainfed lowland

Each MRS population (remove plants with undesirable traits)

Irrigated(YP)

Rainfed upland

Biotic stresses

Continued introgression breeding/DQP

50% DMS plants

New MRS for

next round

Genotyping for gene/QTL

discovery, confirmation and

monitoring trait improvement

New lines for PYT

Improved lines for PT

New ILs/PLs

RYT and NCT under different target Es

Farmers in dif. target Es

Continuation

of MRS

Breeding Procedure of Molecular Recurrent Selection (MRS)

50% fertile plants

Screen for biotic stress resistances

Random mating

Screening abiotic stress tolerances

Multiple MRS populations

Yield traits

Screen quality traits Superior

ILs/PLs

Continued IB and

pyramiding50% MS plants

Genome selection and trait design and

improvement based on genetic information

of the parents of MRS populationsMaterial platform for

large scale MB

Technology for pyramiding multiple

genes/traits and quick progeny

fixation based on combined genome

and phenotypic selection

NS

NS

PS

Random mating

population for

next round MRS

SNP genotyping、、、、gene/QTL

discovery、、、、allelic mining and

confirmation, trait design and

improvement

Preliminary yield trial of promising lines

Cross progeny testing for multiple traits and

confirmation

Multi-location yield trials of promising lines

Demonstration & PVS in the target environments

Continued

MRS

Genome selection and trait design and

improvement based on genetic information

of the parents of MRS populations

Genome sequence information platform of the rice core collection

Technology for pyramiding multiple

genes/traits and quick progeny

fixation based on combined genome

and phenotypic selection

PS = positive

selection

NS = negative

selection

PS

NS

Conclusions

• There are tremendous amounts of hidden genetic

diversity for almost all complex phenotypes in the

primary gene pool, and selection of parental lines

based on phenotype practiced by most breeders is a

poor way to exploit this hidden diversity.Development of rice cultivarsn and

discovery of genes/QTLs for complex

• The genetic network for complex phenotypes are

very complex - large number of loci and multiple

functional alleles at most of the loci.

• Backcross breeding, effective selection (screening)

combined with DNA markers are the effective way

to discover and exploit this hidden diversity.

discovery of genes/QTLs for complex

phenotypes can be and should be

integrated.

Thank you for your attention!

HLONG

Stamp

2012 gsr - breeding technology

Education

unimproved

high yieldwidely

individual

location yield

severe drought

bc2f4 bulk

primary gene

bc populations