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
Geranylgeranyl
diphospate AS
CPS GA12 -aldehyde
GA7ox
ent - Copalyl diphosphate
GA 12
KS
KS GA13ox
ent -Kaurene GA 53
ent -Kaurenol GA 15 GA 44
KO
KO GA
ent -Kaurenal C20ox GA 19
GA 24 sd-1
ent -Kaurenoic acid GA 9 GA 20
KAO
KAO
GA3ox
ent -7a-hydroxy
kaurenoic acid GA4 GA 1

Subjects

Introduction

Concept of GSR

GSR Breeding Strategy and
Technology
Perspectives

The impact of ‘Green Revolution’ in China

60000
Impact of ‘Green Revolution’ Impact of hybrid rice
50000

40000

30000
Yield

20000

10000

0
1965
1967
1969
1971
1973
1975
1977
1979
1981
1983
1985
1988
1990
1992
1994
1996
1998
2000
2002
Year

Yield/unit area
Total production

Important problems in rice
production worldwide

• Increasing problems in abiotic and biotic
stresses
• Over-use of pesticides
• Abuse of chemical fertilizers
• Shortage of water
• Ever increasing demands for yield increase
• Urgent need for improved quality

In China
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

Fertilizer application and grain production in China

Total grain production（in
10000 t）、unit area yield
4500 75000

production（
70000
4000
Fertilizer use 65000
Fertilizer use (in 10000t)

3500 Grain production
Grain yield per unit area 60000

(kg/10ha）
）
3000 55000

）、unit
50000
2500
45000

）、
2000
40000
1500 35000
30000
1000
25000
500
20000
0 15000
1975 1978 1982 1985 1988 1991 1994 1997 2000

Trends of rice production and uses of pesticides
and fertilizers in China in the last 30 years
40 150 50

Fertilizers （million ton）
）
7 35 单产 45
130

Pesticides（10000 ton）
）
农药 40
Yield（ton/ha）
（ton/ha）

30 化肥 110
6 35
25
90 30
20

（
5 70 25
15
20
50
4 10 15
5 30
10
3 0 10 5
1978 1981 1984 1981 1984 1987 1990 1993 1996 1999 2002 2005
1975 1978 1987 1990 1993 1996 1999 2002 2005

5

Grain yield(ton/hm2)
Grain yield per unit area
Grain yield/ha
4
/

3

2

1
1961 1966 1971 1976 1981 1986 1991 1996 2001 2006
350 350
350 350

Nitrogen use efficiency (kg/kg )
Nitrogen consumption(kg/hm2 )

300 氮肥用量 300
300 300

）
公顷）

PFP
250 N consumption 250

kg/kg
250 250
/

200
NUE 200
200 200

氮肥生产效率（
氮肥用量（公斤

150 150
150 150
100 100
100 100
50 50
50 50
0 0
0 0
1961 1966 1971 1976 1981 1986 1991 1996 2001 2006
1961 1966 1971 1976 1981 1986 1991 1996 2001 2006

Annual yield losses

~20% from abiotic stress: drought,
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.

Which places have been left out by Green
Revolution: Rice Yield Gaps in Irrigated and
Rainfed Ecosystems in Asia, 1967-97
6.0
Irrigated Rainfed

5.0 Irrigated 100
(40%)

4.0 80
Y ie ld (t/h a )

Largely Irrigated
(30%) 60
3.0

40
2.0

20
Rainfed
1.0 (30%)
0
MC TC
0.0
1967 1970 1973 1976 1979 1982 1985 1988 1991 1994 1997
Adoption percentage
Year
of modern cultivars
Source: M. Hossain, IRRI

Consequences of the
Green Revolution
Productivity

Diversity

Chinese scientists are calling
“Second Green Revolution”
Less inputs, more production, and
environmental sustainability
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.
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)

To develop GSR rice varieties, breeders
are facing the following challenges:

Many target traits:
Yield and its related traits
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

10% of 22 wild species

27% of
modern
varieties

90% of the 73% of
Cultivated rice landraces

Everson et al. 1998

Status of the International Rice
Genebank Collection at IRRI
Incoming
Accessions Total
samples

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 scored
accessions (n=79,925)
100
90
80
70
60
50
40
30
20
10
0
44 morpho-agronomic traits

No. accessions

20,000
10,000
30,000
40,000
Blast 50,000
Bacterial
blight
Sheath
blight
Screened

Rice tungro

BPH 1

BPH 2
Resistant

BPH 3
Green
resistance/tolerances at IRRI

leafhopper
Whitebacked
planthopper
Evaluation of rice germplasm for stress

Cold
tolerance

Cold tolerance (1-3 = tolerant; 5 =
intermediate; 7-9 = susceptible)
2,500
n=6,625
2,000

1,500

1,000

500

0
1 3 5 7 9

Yield responses of the 193 parental lines of IRMBN
to the terminal drought under the lowland condition

25
±
-19.1±44.0%
20

15

10

5

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

Yield reduction (in %)

Establishment of the core collections for
major crops in the CAAS’s genebank
Core collections of rice, wheat, corn and Indica

soybean were established with only 5% of
the accessions representing over 90% Jap M.
.

Jap U.
.

Jap L.
.

genetic diversity of the whole collections. 0.1
0.1
Japonica
Ind EM.
.
Ind M.
.

Ind M
. L

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%
Comparison of genetic diversity among core collections
with different sampling ratio (Jia jizheng,2004)

Current Status of Characterization and Utilization of
Germplasm Collections in Genebanks Worldwide

Collection and conservation largely completed

Characterization – very superficial
- Phenotypic evaluation and description
To identify accessions with desirable (often extreme)
phenotypes to be used as parents in breeding programs
- Few accessions with desirable phenotypes for most traits
- No accessions with desirable phenotypes for certain traits

How much valuable genetic variation for target traits in
the primary gene pool for breeding remains unclear!

Utilization – very poorly
- Less than 5% of the collected germplasm in the Genebanks
have been utilized in the worldwide breeding programs

Reasons for Poor Utilization of Germplasm
Outstanding commercial genotypes are commonly
destroyed by crosses with unimproved exotic germplasm
(Duvick 1984)
Slow but consistent genetic improvement can still be
achieved even within a narrow base in many breeding
programs
Selection of parental lines in breeding programs are largely
based on phenotype and very few accessions appear to have
“desirable” phenotype for complex traits

The GSR Breeding Strategy: Exploiting
the maximum genetic diversity in the
primary gene pool of rice
Objectives
To exam if there is sufficient (novel) genetic
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
- Integration with the molecular tools
- Integration with gene discovery
- Generation of information and training personnel

The Basic Idea
Full Exploitation of The Genetic Diversity in the
Primary Gene Pool of Rice

The GSR Breeding Strategy
Recipients Donors
(46 best commercial X (203 WMCC, 300 CMC +
Varieties and hybrid parents) 20 wild rice accessions)
Genotyping by re-
BC breeding to introgress sequencing of all
superior alleles from MCC into parents
elite genetic backgrounds

Parents for next Trait-specific Molecular database
round of DQP IL sets in elite GBs of the parents

Genotyping &
phenotyping

Development of
Genetic characterization
new cultivars of ILs
Breeding by MRS
and PL sets or DQP
-omics and
bioiformatics
Release to Theory and
technology of
farmers breeding by
Gene networks and metabolic
molecular design 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 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;
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.

Two Fundamental Questions:

• How much useful genetic diversity,
particular for the complex
phenotypes, within the primary
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 Add new genes/traits IR64 introgression
by backcross breeding
adaptable lines with improved
high yield target traits
varieties (IR64)

IR64 lines with improved Discovery of desirable QTLs using
target traits and the “same” DNA markers and MAS for
pyramiding QTLs
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
X
Self and bulk
harvest
~25 BC1F2s x RP ~25 BC2F1s x RP
X Self and bulk
harvest
Bulk BC1F2 populations Bulk BC2F2 populations

Screen for
target traits: 1, 2, 3, 4, 5, n 1, 2, 3, 4, 5, n

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

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

Genotyped w/ DNA markers to track the gene
flow and to identify genes/QTLs for the target
traits

Promising ILs with selected target Best ILs with selected target trait(s)
trait(s) and good yield performances used as parental lines for
nominated for NCTs pyramiding genes/QTLs from
different donors

Development and releases of
green super rice cultivars for To rice farmers in the target
specific target environments 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,
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)
I (indica)
Sub-G3 (33)
Sub-G4 (46)
Ba-Bao-Mi (Yunnan)
Sub-G5(15)
II (japonica)
Sub-G6 (12)
Sub-G7 (28)
Sub-G8 (9) III (New group)
Jalmagna (India)

Gene diversity of the donor gene pool
Proportions of accessions Relative genetic diversity of
from different geographic accessions in different
regions geographic regions
Europe America Others Europe America Others
15% 10%
NA NA

SA SA
China 33% China 40%
22% 26%
SEA SEA
30% 24%

Target traits

• Tolerances to drought, salinity, submergence,
zinc deficiency, phosphorus deficiency,
anaerobic germination, etc.

• Resistances to BB, BPH, blast, tungro, sheath
blight, etc.

• Yield and related traits
• Different maturities
• Different types of grain quality parameters

BC Breeding Procedure
RP X Donors of diverse origins

F1s X RP

BC1F1 X RP

BC2F1
x
BC2F2 bulk populations

Selection for target traits

Progeny testing Survival plants Genotyping

Major differences of introgression breeding and
the conventional BC breeding
BC breeding Marker aided Introgression
BC breeding breeding
RP selection Elite Same Same
Donor selection Yes Yes No/diverse

Target traits Single Single or few No limitation
monogenic/dominant
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
progenies

Screening of BC2F2 populations for tolerance
to terminal drought at the reproductive stage
under the lowland conditions
Stress for 20 days (March 27,2001) Stress for 56 days (May 2, 2001)

Variation in BC2F2 populations for drought
tolerance under the lowland conditions

Summary of selected drought tolerant BC2F2 plants
under lowland stress conditions

NPT IR64 Teqing Total
Total plants selected 897 2775 489 4161

# of selected plants 8.5 22.4 6.3 13.2
per population (3.8%) (10.0%) (3.0%) (6.8%)
Range 0 - 85 0 - 100 0 - 30 0 - 100
No. of populations 113 124 105 320
No. of I donors 59 67 59 185
No. of J donors 32 45 19 96

Contributing donor (%) 80.5 90.3 74.3 87.8

The Screening of BC2F2 populations
under upland drought conditions

The RP, IR64


IR64 Teqing Total
Total plants selected 192 334 526
Ave. selected plants 9.6 (4.6%) 10.8 (5.2%) 10.3 (5.0%)
Per population
Range 4 - 20 3 - 15 4 - 30
No. of populations 20 31 51
No. of I donors 12 23 35

No. of J donors 8 8 16

Contributing donor (%) 100 100 100

Parental performances and 442 selected DT BC2F2
plants for drought tolerance from 19 BC populations
VG Donors Origin IR64 (S) Teqing (M) NPT(SS)
Total
LL (UL) LL (UL) LL
I BR24 (S) Bangladesh 14 (27) 12 (7) 3 29 (34)
I STYH (S) Myanmar 20 (26) - 4 24 (26)
I OM1723 (S) Vietnam 7 (17) 7 (6) 0 14 (23)
J FR13A (SS) India 15 (16) 17 (15) 0 32 (31)
J Type3 (SS) India 23 (15) 10 (12) 0 33 (27)
J Binam (M) Iran 20 (19) 14 (13) 1 35 (32)
J HAN (M) China 11 (13) - 3 14 (13)
I Zihui100 (S) China 8 - 9 17
J Khazar (S) Iran 58 - 58
Total 176 (133) 60 (53) 22 256 (186)

Screening of BC2F2 populations for salinity
tolerance at the seedling stage

Young seedlings were subjected to:
IR64 ST CK
6 dSm-1 for 3 days, 12 dSm-1 for 2 weeks, 18
Pokali
dSm-1 for 1 week, and 24 dSm-1 for 1 week

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

Summary results of BC populations
for screening salinity tolerance
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

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

Summary results of BC populations
for screening anaerobic germination
and submergence tolerance
Anaerobic germination Submergence


# 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
Selected lines 31 67 77 175 538 431 451 1411
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
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.

Summary results of BC populations for screening
low temperature germination and BPH resistance

Low temperature germination BHP resistance


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

# of selections per pop. 0 - 21 0 - 18 0 - 31 0 - 22 0 - 22 0-2


# 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

BC2F4 progeny testing under very severe
Details BC2F2 screening under moderate field stress 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
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

Screening for blast resistance

Low N stress
experiment
under rain-off
shelter

Improving japonica for cold
tolerance at the reproductive stage

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)

No. of SF (%)
Population SI 1
Donor parent Subspecies Code selected
size
plants
(%) 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
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
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.

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)

Cold stress at the seedling
No. of stage Cold stress at the reproductive stage
Donor parent selected Survival rate of seedlings
lines (%) 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

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

Comparison of selection efficiencies of 11 CY1 BC2F6 populations for cold
tolerances at the seedling and reproductive stages

The reproductive stage The seedling stage
Population
N1 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 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
1N 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.

Mean performances of 116 ILs of five populations for 11 traits evaluated under
normal and cold water stress conditions in 2010
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
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

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
GY GW HD HI PH SF
BM (g/plant) FGN PN SNP
Donor N1 Treat (g/plant) (g) (d) (%) (cm) (%)

N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2
Chhomrong 24 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 S 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

Total 116 91 1 89 0 77 0 59 6 88 11 74 9 102 2 22 34 94 0 28 38
Chhomrong 24 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
N
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

1N 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.

Mean performances of 19 promising ILs under cold water stress and
normal conditions in 2009 and 2010 (Meng et al. 2012)

Line# Pop.1 2010 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 G 134.2 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 F 126.5 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 F 131.7 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 F 133.4 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 F 129.3 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 G 122.0 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 G 121.0 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 136.7 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 E 137.8 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 F 129.5 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 G 132.6 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

LW264 I 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 I 130.7 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 E 138.9 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

LW151 E 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 G 132.4 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

LW216 G 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

LW200 G 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

LW291 I 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

Reactions (lesion lengths) of HHZ and two donors to 14
tropical races of BLB caused by Xanthomonas oryzae pv oryzae

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

PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO aver
61 86 79 340 71 112 99 145 280 339 341 347 349 363 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

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）

F1-F5
F1- F6-
F6-F10 F11-
F11-F15 F1-
F1-F5 F6-
F6-F10 F11-
F11-F15 F1-F5
F1- F6-
F6-F10 F11-F15
F11-

对部分小种抗病的株系对全部15个小种高抗的株系对全部15个小种感病的株系

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

HHZ is
susceptible to
most tropic
BLB races

Vera Cruz et al

Ten HHZ ILs with broad spectrum resistance to all 14 races
of bacterial blight pathogen, Xanthomonas oryzae pv oryzae

PX PX PX PX PX PX PX PX PX
PX PX PX O34 PX O11 PX O14 O28 O33 O34 O34 O34 O36 aver
O61 O86 O79 0 O71 2 O99 5 0 9 1 7 9 3 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

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

Reactions of 512 HHZ ILs to 14 tropical Xoo races

Race R% (LL <3.0 cm)
P1 76.4
P2 4.7
P3b 4.9
P3c 4.9
P4 22.4
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

Classification of 14 Xoo races into two major groups (virulent
and less virulent ones) based on the reactions of the 512 HHZ ILs

P1
P5
Weak virulence group
P4
P7
Name Xoo races

P8
P10
P2
P9c
P6
P3c
High virulence group
P3b
P9a
P9b

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
Average Distance Between Clusters

Classification of the 512 ILs based on their resistances to the 14 Xoo Phillipines races
H9-39
H5-1
H8-27
H9-20
H17-65
H9-3
H9-13
H5-32
H8-44
H15-12
H17-29
H5-49
H15-1
H8-8
H8-23
H9-7
H8-13
H8-51
H9-16
H9-26
H5-12
H5-13
H8-3
H19-48
H17-11
H12-27
H8-33
H5-5
H15-26
H9-24
H5-51
H8-21
H8-31
H5-59
H8-47
H9-14
H9-25
H5-6
H8-41
H9-18
H8-40
H8-26
H12-17
H19-18
H9-56
H19-22
H19-23
H5-26
H17-32
H11-10
H12-26
H9-40
H8-55
H12-16
H11-32
H11-30
H11-36
H11-34
H11-45
H11-49
H12-39
H19-45
H12-2
H11-28
H9-70
H15-43
H17-35
H19-55
H19-13
H11-31
H19-15
H12-24
H9-41
H12-20
H19-46
H12-18
H19-29
H9-51
H11-16
H19-14
H17-34
H9-9
H8-38
H11-50
H12-40
H12-61
H12-55
H17-5
H15-19
H12-64
H15-21
H19-57
H19-50
H9-66
H19-59
H19-36
H15-8
H15-25
H12-54
H15-24
H19-56
H17-53
H9-4
H15-30
H5-55
H8-18
H15-11
H12-31
H5-60
Name of lines

H8-54
H11-54
H12-36
H19-35
H11-11
H11-55
H12-48
H11-24
H12-9
H12-4
H12-7
H12-15
H19-9
H8-45
H11-27
H9-63
H12-12
H12-33
H12-42
H11-33
H17-54
H9-37
H11-21
H9-6
H11-25
H19-7
H12-13
H19-4
H8-10
H8-42
H12-28
H12-65
H15-31
H17-1
H8-52
H12-5
H5-75
H11-17
H11-19
H12-29
H5-11
H5-74
H5-18
H5-21
H17-38
H8-50
H9-15
H8-46
H12-45
H17-64
H5-29
H19-1
H8-12
H11-5
H12-49
H19-47
H8-7
H12-14
H19-16
H5-33
H8-53
H9-19
H9-21
H5-54
H17-63
H8-15
H8-35
H5-41
H11-37
H11-40
H9-22
H11-38
H17-9
H17-19
H17-14
H17-24
H17-13
H17-21
H17-49
H17-52
H17-39
H17-48
H17-62
H9-38
H17-57
H17-28
H17-45
H15-44
H5-3
H5-23
H9-12
H8-28
H5-36
H5-35
H8-39
H15-6
H15-9
H5-61
H17-60
H5-66
H5-67
H17-68
H17-66
H5-48
H5-53
H15-33
H17-36
H5-28
H5-52
H8-22
H5-42
H9-17
H5-10
H8-30
H5-63
H5-72
H11-23
H9-32
H5-15
H17-40
H5-39
H15-32
H17-18
H5-43
H8-6
H5-65
H8-34
H8-36
H12-58
H19-5
H15-13
H9-23
H15-35
H19-19
H15-40
H15-42
H15-38
H19-58
H19-62

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
Average Distance Between Clusters

Are the parental performances
correlated with the performances
of their BC progenies?

Genetic background effects in
introgression breeding

Submergence Tolerance
Number of submergence tolerant plants in 9 BC2F2
and 3 BC3F2 populations under the field condition
VG Donors Origin TKM9 (SS) Khazar (SS) FR13A (T) Total
(I) (I) (J)
I IR64 (S) India 12 8 14 34

I Teqing (SS) India 10 9 8 27
NPT (SS)
J Iran 6 6 6 18
BC2F2
NPT (SS)
J Iran 10 71 2 83
BC3F2
Total 38 94 30 162

Yield responses of the 193 parental lines of IRMBP
to the terminal drought under the lowland condition

25
±
-19.1±44.0%
20

15

10

5

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

Yield reduction (in %)


NPT IR64 Teqing Total
Total plants selected 897 2775 489 4161

# of selected plants 8.5 22.4 6.3 13.2
per population (3.8%) (10.0%) (3.0%) (6.8%)
Range 0 - 85 0 - 100 0 - 30 0 - 100
No. of populations 113 124 105 320
No. of I donors 59 67 59 185
No. of J donors 32 45 19 96

Contributing donors (%) 80.5 90.3 74.3 87.8

Parental performance and 442 selected DT BC2F2
plants for drought tolerance from 19 BC populations
VG Donors Origin IR64 (S) Teqing (M) NPT(SS)
Total
LL (UL) LL (UL) LL
I BR24 (MR) Bangladesh 14 (27) 12 (7) 3 29 (34)
I STYH (S) Myanmar 20 (26) - 4 24 (26)
I OM1723 (S) Vietnam 7 (17) 7 (6) 0 14 (23)
J FR13A (SS) India 15 (16) 17 (15) 0 32 (31)
J Type3 (S) India 23 (15) 10 (12) 0 33 (27)
J Binam (M) Iran 20 (19) 14 (13) 1 35 (32)
J HAN (M) China 11 (13) - 3 14 (13)
I Zihui100 (S) China 8 - 9 17
J Khazar (MR) Iran 58 - 58
Total 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 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).

Seedling Cold Tolerance (from NARES)
Selection of 861 C418 plants with seedling cold tolerance
from 28 C418 BC2F2 populations 2002 (LAAS)
Non-CT
BC2F2 CT donors
donors
# of populations 28 2 26
# of surviving plants
10.3% 14% 0.3
per population
Range 1.4 – 19.3% 10 – 16% 0 – 3.0%
# of surviving plants
10.3% 7.6% 10.5%
per BC population
The mean population size was 310, ranging from 196 – 465, the
recipient, C418 (japonica) was killed by the stress.

Genetic background effects on the
performance of BC progenies
Teqing / Chipda NPT / Chipda

Donor and recipient effects on the number of BC2F2 plants
selected under lowland drought during the 2002 dry season
Donor Recurrent parent Donor Recurrent parent

IR64 Teqing NPT IR64 Teqing NPT
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***

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*

Genetic background effects on the number of survival plants under submergence
in 33 BC4F2 populations from crosses between 3 RPs and 11 donors
Cross Survival (%) Z value Cross Survival(%) Z value
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
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?

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

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

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

Donor 1 N SI (%) 2 Mean 3 Range N 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

9 2.25 38.1 abcd 19.5–50.0 192.5 ab 143.3–275.5
X21 (I) 29 6.44 64.3 cd 50.6 - 87.1

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

Q5 (I) 31 6.89 71.1 abc 50.9 - 91.4 6 1.50 41.1 abc 19.9–75.4 160.4–274.2

Chhomrong (J) 24 5.33 51.4 - 87.8 17 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 - 98.5 12 3.00 31.3–70.1 180.7 abc 138.2–238.0

9 2.25 28.9 d 17.0–44.4 171.5 abc 112.0–216.7
Shennong265 (J) 21 4.67 69.2 abcd 50.7 - 93.8
25 6.25 45.5 ab 23.9–65.6 83.2–255.4
Yuangeng7 (J) 41 9.11 71.1 abc 50.0 - 90.1
13 3.25 33.0 cd 17.0–48.9 171.9 abc 111.6–230.4
OM997 (I) 21 4.67 72.1 ab 54.9 - 89.6
8 2.00 33.6 abcd 24.9–48.3 175.5 abc 121.4–280.4
Cs94 (I) 19 4.22 64.2 cd 51.4 - 86.0
124 3.44
5.2 e 0.0–7.9 157.4 bc 127.4–178.6
Chaoyou (J) 324 6.55 24.8 e 19.0 - 30.0

2N 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.

Trait specific introgression lines developed
# of BC2F2 No. of selected
Target traits
populations BC2F3 lines

Drought tolerance 350 4687
BPH resistance 203 522
Salinity tolerance 203 1022
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
progenies;

• More distantly related donors, particularly
landraces, tend to give more transgressive
segregations for abiotic tolerance in the BC
progenies.

Conclusions
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
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
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)

DT C418 ILs Check (C418)

Progeny Testing Under Stress
(no irrigation after transplanting)

Promising DT C418 ILs

2001-2002 DS BC2F4 progeny testing

IR64 ILs for quality IR64 (CK) DT IR64 ILs

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 program

The Recurrent Parents
C418
Liaojing454
(restorer)

Preliminary Yield Trials of Promising
DT/WUE ILs
30%
water
saving

70%
50% water
water saving
saving

Replicated Preliminary yield trial of DT/WUE ILs
(Shengyang/2006.9)
Completely Water
rainfed saving
70%

Water Water
saving saving
50% 30%

Promising DT/WUE 辽粳9号对照
辽粳号对照
IL -HR95

抗旱导入系的节水实验

Yield performances of two promising DT/WUE
ILs in replicated yield trials under stress and
non-stress conditions (Shengyang/2006)
25
Yield change over CK (%)

20 Normal irrigation

15 30% water saving
10
50% water saving
5
70% water saving
0
Completely rainfed
-5
HR94 HR95 Liaojing 9
(CK)
in Liaojing 454background

Yield potential and DT/WUE of DT ILs
% change
over CK Rainfed 70% 50% 30% Normal
25

20

15

10

5

0

-5

-10
HR354 HR525 HR9 HR94 HR95 LJ9
(C418) (C418) (C418) (LJ454) (LJ454) (CK)

Promising DT/WUE FAZ ILs

Zhonghua 1 Zhonghua 2

GSR material ST in Infanta

• GSR material

• material (572 lines)

• Other group’s material

2011-10-20
Lijun Meng

2012 GSR - breeding technology

High EC Low EC

GS NON-
s
R GSR
e
a

NON GSR material

GSR material

HHZ HHZ HHZ HHZ 23-Sal8-DT1-ST1

R1 R2

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

2011-10-7

HHZ 24-DT6-DT1- IR 63307-4B-4-3 HHZ 23-DT14-DT1-DT1
DT1

2011-10-7

HHZ 25-SAL9-Y3-ST1

Introgression Breeding for
improving 2 or more
complex traits

RP X Donors

BC2F1
X

BC2F2

Screening under Screening under Screening under Selection for high yield
severe salinity submergence severe drought under normal condition

ST ILs SUBT ILs DT ILs HY ILs

PT under severe PT under PT under severe PT for high yield under
salinity submergence drought normal condition

Promising ILs with more than one target traits to be
tested in multi-location yield trials in target Es

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

Mozambique
Cote D’ivoir

Bangladesh

Philippines
Indonesia
Tanzania

Pakistan
Vietnam
Rwanda

Nigeria
Mali

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) 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
06WS First batch of 8 HHZ BC1F2 populations (08WS)

08WS Yield traits DT screen ST screen SUB screen Random plants
1st round
selection 82 HY plants 109 DT plants 120 ST plants 3 SUBT plants

QTL/Allelic
311 genotyped/progeny tested for all target traits diversity
discovery
09DS 212 Yield 153 DT screen 211 ST screen 171 SUB screen
for target
2nd round traits
selection

09WS 495 genotyped/progeny tested for all target traits
3rd round
selection Confirming genetic
10DS 12 RYT and 108 PYT under DT, low input, NC networks for target
traits and their
genetic relationships
68 promising ILs
Used as parents for
designed QTL
68 replicated 2 NCT
10WS/11DS 3 Demo pyramiding
yield trials in 11WS

The Introgression Breeding Procedure
06WS Second batch of 8 HHZ BC1F2 populations (09WS)

08WS Yield traits DT screen ST screen SUB screen Random plants

119 HY plants 210 DT plants 314 ST plants 21 SUBT plants
QTL/Allelic
664 genotyped/progeny tested for all target traits diversity
discovery
for target
10DS Yield under DT screen ST screen SUB screen
NC & LI
traits

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

Confirming genetic
10WS 865 genotyped/progeny tested for all target traits networks for target
traits and their
232 yield genetic relationships
130 DT screen ST screen SUB screen
11DS under NC&LI

305 HY&FUE ILs 570 DT ILs ST ILs SUB ILs

RYT & Promising ILs as parents for
11WS DEMO
PYT
designed QTL pyramiding

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 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

Trait specific HHZ ILs developed in
CAAS and IRRI in 4 years
Number of
Traits Institution ILs selected
donors
CAAS 8 180
Drought tolerance
IRRI 15 978
CAAS 40 1200
Salt tolerance
IRRI 15 633
Tolerance to low inputs IRRI 250 350
Submergence tolerance IRRI 4 121
CAAS 8 210
High yield
IRRI 15 610
High yield under low
IRRI 451 451
inputs
CAAS 40 1809
Total
IRRI 15 1260

Performances of some high yield HHZ
ILs under irrigated conditions at IRRI

Grain Yield (t/ha)
Mean % over
Designation over % over NSICRc1
2010WS 2011DS
seasons IR72 58
HHZ8-SAL6-SAL3-Y2 6.55ab 8.0ab 7.28 10.56 12.27
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)

The HHZ ILs in RYT have diverse grain pasting properties
suitable for consumers with different taste preferences
1 2
6000 120
3 4
5 6
5000
100 7 8
9 10
4000
11 12
80
13 14
Viscosity, cP

Temperature
3000
15 16
60 17 18
2000 19 20
21 22
40
1000 23 24
25 26
20 27 28
0
0 100 200 300 400 500 600 700 800 29 30
31 32
-1000 0
Tim e, sec 33 34
35 36
AC=14.5-31.6%; GT= H-I-L; Protein=7.8-11.2%

Development of ILs with resistances to multiple
abiotic/biotic stresses
BC2F2Bulk populations

Screen for the Drought screen – DT ILs Genotyping
primary target trait

Screen for
Yield related Disease and QTL & QTL
other traits Salinity
traits insect resistances networks for
target and non-
target traits
Promising ILs with multiple
desirable traits (QTLs)

Parents for DQP Promising lines

Breeding by Yield trials at
DQP procedures multiple locations

Development of IR64 ILs with multiple desirable traits
IR# RP(%) Donor BPHR SBR ST SUB Yield/plant (g)
(Score) (LL, cm) (Score) (%) 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
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 -

Question:

• When we are trying to improve
more than one complex trait, what
trait(s) should be selected first,
yield or abiotic/biotic stresses?

HHZ x Donors (1=IR64 , 2=AT354 , 3=C418)
Population F1 x HHZ
development and 25 BC1F1 x HHZ
selection 25 BC2F1
X

3 bulk BC2F2s (480)

2010 Beijing Summer
1: DT (19) 1: HY (26) 1: ST (57)
2: DT (29) 2: HY (28) 2: ST (49) BC2F3s
1st selection
3: DT (33) 3: HY (29) 3: ST (56)

2010 Beijing Summer 2010 Hainan Winter 2010 Winter phytotron
1: HY (0) 1: DT (12) 1: HY (2) 1: DT (0) 1: ST (25)
2st selection BC2F4s
2: HY (2) 2: DT (23) 2: HY (1) 2: DT (0) 2: ST (28)
3: HY (3) 3: DT (8) 3: HY (2) 3: DT (1) 3: ST (29)

2010 Hainan Winter 2010 Hainan Winter
1: HY (0) 1: DT (0) 1: DT (3) 1: HY (3)
2: HY (2) 2: DT (0) 2: DT (4) 2: HY (5) BC2F5s
3nd selection
3: HY (1) 3: DT (2) 3: DT (2) 3: HY (2)

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

N Mean 23.4±0.6 175.4±16.1 192.0±18.3 90.7±1.8 8.3±1.2 22.0±1.3
HHZ 116.2±3.2 75.6±1.4
(RP)
S Mean 21.0±0.4 137.1±13.7 154.4±14.2 86.4±2.0 8.8±1.2 17.6±0.7
107.3±11.5 74..0±1.6

Mean 22.5±3.0 171.9±47.6 197.3±49.3 86.8±5.5 7.9±1.6 22.7±6.6
111.8±5.1 75.6±4.4
N
Range 15.2-26.0 106.7-255.8 136.3-272.4 74.4-93.8 6.2-10.6 12.8-32.6
101.0-111.0 66.3-78.9
IR64 26
Mean 20.2±1.8 135.1±31.8 154.3±30.2 74.3±11.2 9.2±2.3 ±
14.8±5.2
91.3±5.2 71.3±4.7
S
Range 17.5-22.6 80.2-194. 9 98.1-203.6 49.4-91. 4.4-14.3 4.3-23.9
78.0-99.5 65.0-77. 5
Mean 20.3±1.0 184.8±28.8 231.0±31.4 79.9±4.3 10.2±1.6 27.6±5.5
107.1±7.3 72.5±2.3
N
Range 19.0-22.0 127.8-217.8 166.7-273. 1 72.7-85.7 8.7-12.3 19.3-35.0
AT354 28 98.5-110 69.2-74.8

Mean 18.6±1.2 119.1±19.7 145.3±26.4 63.3±13.4 9.6±1.9 ±
10.9±3.6
90.1±7.0 65.7±3.9
S
Range 17.1-20.5 73.4-156.1 101.6-176.5 51.1-80.2 7.3-12.5 6.9-19.1
82.0-99.0 58.5-68.9
Mean 23.2±1.7 192.1±36.3 217.2±40.0 88.4±5.3 7.8±1.5 24.4±5.7
111.6±4.3 76.2±3.7
N
Range 20.6-26.1 99.7-228. 7 142.4±270.6 70.4-92.5 4.6-11.7 13.9-40.4
C418 29 99.5-117.5 76.4-81.2
Mean 20.8±1.5 143.6±28.8 155.4±24.4 79.2±12.1 9.2±1.6 18.7±5.9
97.7±5.7 75.4±5.5
S
Range 18.0-23.0 87.1-175.7 114.2-197.3 55.6-89.7 7.2-11.8 7.6-26.5
86.5-103 69.7-80.4

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
HD PH GW FGW SNP SF PN GY
Donor T N1
N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2

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

AT354 N 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

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

AT354 S 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.

Performances of some promising DT ILs under drought stress and normal
conditions in Beijing and Hainan, 2010
Under the normal condition Under the drought stress condition
L Donor Line# TG
HD PH TGW FGN SNP SF PN GY HD PH FGN SNP SF PN GY
W
HHZ 115.3 - 23.1 172.8 189.0 91.4 7.6 23.1 - - - - - - - -
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
AT354
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

BJ 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
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
C418
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
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

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

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

10.
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 71.3 16.4
4
AT354
11.
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 85.8 21.6
6

HN 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

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
C418
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
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.

Uses of ILs for
pyramiding genes/traits
from 2 or more donors to
develop GSR varieties

Experimental design for simultaneous improvement of
DT, ST and yield potential by pyramiding
IL1(HY, DT) x IL2(HY, DT) IL3(HY, ST) x IL4(HY, ST)

F2 F2

Screen Screen Select for Screen Screen Select for
for DT for ST HY and for DT for ST HY and
random random
DT ST DT ST
PDLs PDLs PDLs PDLs

Genotyping and progeny Genotyping and progeny
testing for all target traits testing for all target traits

HY, DT, ST
HY, DT, ST
PDLs (PDL1)
Discovering genetic networks for HY, DT, PDLs (PDL2)
ST and their genetic overlap

Designed QTL pyramiding based on the genetic and
phenotypic information of parental ILs
IR64/BR24//IR64///IR64 IR64/Binam//IR64///IR64
BC2F2 BC2F2

Screening under drought

Genotyping X
Genotyping
DT IR64/BR24 IL DT IR64/Binam IL
and QTL and QTL
identification identification
F1
X

F2

Screening under severe drought

Progeny testing Survival plants Genotyping

Pyramiding F2 population screened under
severe lowland drought at the reproductive
stage (2002-03 DS)
IL1 F2 IL2

An average of 25% of the progeny of the 9 F2
populations survived the severe drought stress

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
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

8.0 Control 2.0
Terminal stress
6.0 1.6

1.2
4.0
0.8
2.0
0.4

0 0
GG1 GG2 GG4 GG3 IR64 GG1 GG2 GG4 GG3 IR64

±
GG1 (X = 109±20, 66%) ±
GG1 (X = 35±8, 361%)
±
GG2 (X = 247±35, 149%) ±
GG2 (X = 33±12, 344%)
±
GG4 (X = 117±18, 70%) ±
GG4 (X = 34±8, 373%)
±
GG3 (X = 140±33, 84%) ±
GG3 (X = 35±13, 364%)
±
IR64 (X=166±10, 100%) ±
IR64 (X=9.7±5, 100%)

ANOVA Result for Yield of 2004 Dry Season

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
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

Yield performances of the 4 group genotypes under the rainfed
upland stress and non-stress conditions in 2004 wet-season

Control Stress
500 160
140
400 120
300 100
80
200 60
100 40
20
0 0
GG1 GG2 GG3 GG4 IR64 GG1 GG2 GG3 GG4 IR64

±
GG1 (X=124±20, 51%) ±
GG1 (X=50±22, 1111%)
±
GG2 (X=310±34, 129%) ±
GG2 (X=44±24, 978%)
±
GG4 (X=122±44, 51%) ±
GG4 (X=62±31, 1378%)
±
GG3 (X=212±37, 88%) ±
GG3 (X=55±19, 1222%)
±
IR64 (X=241±27, 100%) ±
IR64 (X=4.5±8, 100%)

ANOVA Results for Yield of 2004 Wet Season
YIELD
Source DF MS F P>F R2(%)
Stress 1 2491548.9 1676.0 0.0001 40.4
Group 3 219664.3 147.8 0.0001 10.7
Group(Line) 83 3057.4 2.06 0.0001 4.1
Stress*Group 3 259596.4 174.6 0.0001 12.6
Stress*Group(Line) 83 4307.3 2.9 0.0001 5.8
Stress
Group 3 5626.6 4.26 0.0011 6.9
Group(Line) 83 1773.4 1.34 0.0527 36.3
Control
Group 3 464372.9 292.2 0.0001 65.3
Group(Line) 83 5591.6 3.52 0.0001 21.8

Yield performance of the 4 group genotypes under
mild stress in 2005 dry-season
Stress Control
8.0

6.0

4.0

2.0

0
GG1 GG2 GG4 GG3 CK GG1 GG2 GG4 GG3 CK

±
GG1 (X=237±58, 149%) 151% ±
GG1 (X=157±29, 75%)
±
GG2 (X=313±46, 197%) 127% ±
GG2 (X=247±33, 119%)
±
GG4 (X=227±47, 143%) 131% ±
GG4 (X=173±38, 83%)
±
GG3 (X=249±50, 157%) 152% ±
GG3 (X=164±28, 79%)
±
IR64 (X=159±40, 100%) 76% ±
IR64 (X=208±57, 100%)

Summarized Results from 1st round
pyramiding breeding

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

Summary
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;

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.

Summarized results

• 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

• 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 F2
populations
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
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)
Non-stress Stress
Donor1 Donor2 Donor3 Donor4
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 F2
populations under severe lowland stress
(2005-2006 dry season)

F2 population Male Female IR64
PDL1 PDL2

F2 population

Parental ILs and IR64

Field screening of the 2nd round DQP F2
populations under severe upland stress
(2005-2006 dry season)

Field screening of the 2nd round DQP F2 populations
under severe upland stress (05-06 dry season)
Controlled irrigated condition

Population

DK47 DK158 IR64

Lowland stress

Population
DK47 DK158 IR64

Field screening of the 2nd round DQP F2 populations
under severe upland stress (05-06 dry season)
Controlled irrigated condition

Population

DK47 DK109 IR64

Lowland stress

Population DK47 DK109 IR64

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

from CMS plants to
from CMS plants to

Bulk harvest seeds
Bulk harvest seeds

be screened for
be screened for

target traits
target traits

Selected plants enter

genotyping and next
Selected plants enter

the progeny testing,
genotyping and next
the progeny testing,

round of RS
round of RS

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

On-going MRS in phase II of the GSR project
Each MRS population consisting of many ILs/PLs of the same elite GB
Each MRS population (remove
plants with undesirable traits)

50% fertile plants 50% DMS plants
Continued
Irrigated Rainfed Rainfed
introgression
Flood Biotic breeding/DQP
(YP) lowland upland prone stresses

New MRS for New
Improved
next round ILs/PLs
lines for PT

New lines for
PYT
Continuation
RYT and NCT of MRS
under different
target Es
Genotyping for gene/QTL
discovery, confirmation and
Farmers in dif. monitoring trait improvement
target Es

Breeding Procedure of Molecular Recurrent
Selection (MRS)

improvement based on genetic information
Genome selection and trait design and
Material platform for Multiple MRS
Technology for pyramiding multiple

of the parents of MRS populations
fixation based on combined genome

large scale MB populations
genes/traits and quick progeny

NS Continued
and phenotypic selection

IB and
50% fertile plants pyramiding
50% MS plants
PS
Screening Screen Screen for
Yield abiotic stress quality biotic stress NS
traits tolerances traits resistances Superior
ILs/PLs
Random mating
Cross progeny testing population for
PS for multiple traits and
next round MRS
confirmation
NS
Preliminary yield trial
of promising lines Continued
MRS
PS = positive
selection Multi-location yield trials Genome
of promising lines sequence
NS = negative 、
SNP genotyping、gene/QTL information
selection 、
discovery、allelic mining and platform of
Demonstration & confirmation, trait design and the rice core
PVS in the target improvement collection
environments

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

•
discovery of genes/QTLs for complex
Backcross breeding, effective selection (screening)
combined with DNA markers are the effective way
phenotypes can be and should be
to discover and exploit this hidden diversity.
integrated.
• The genetic network for complex phenotypes are
very complex - large number of loci and multiple
functional alleles at most of the loci.

2012 GSR - breeding technology

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