Inclusivity Essentials_ Creating Accessible Websites for Nonprofits .pdf
2012 GSR - breeding technology
1. 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
3. 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
4. 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
5. 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
6. 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
8. 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.
9. 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.
10. 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
12. 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).
13. 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)
14. 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
15. Where are the sources
of genetic variation
for improving the
‘green’ traits?
16. 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
17. 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
21. 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 %)
22. 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)
23. 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!
24. 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
25. 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
26. The Basic Idea
Full Exploitation of The Genetic Diversity in the
Primary Gene Pool of Rice
27. 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
28. The Chinese GSR research institutions - China
National Rice Molecular Breeding Network
29. 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.
30. 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.
32. 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)?
33. 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
34. 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
35. 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
36. 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
37. 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)
38. 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%
39. 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
40. 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
41. 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
43. 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)
44. Variation in BC2F2 populations for drought
tolerance under the lowland conditions
45. 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
46. The Screening of BC2F2 populations
under upland drought conditions
The RP, IR64
47. Summary of selected drought tolerant BC2F2 plants
under lowland stress conditions
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
48. 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)
49. 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
51. 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
Selection intensity (%) 4.39 3.67 3.44 3.69
Number of japonica donors 9 9 7 25 3 6 1 10
Selected lines 70 66 44 180 43 123 0 166
Selection intensity (%) 3.89 3.67 3.14 3.60
Number of intermediate donors 4 1 3 8 1 1 2 4
Selected lines 35 5 19 59 33 0 0 33
Selection intensity (%) 4.38 2.50 3.16 3.69
52. Summary results of BC populations
for screening salinity tolerance
BC2F2 screening BC2F3 reconfirmation
IR64 Teqing NPT Total IR64 Teqing NPT Total
# 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.
53. 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
54. Summary results of BC populations
for screening anaerobic germination
and submergence tolerance
Anaerobic germination Submergence
IR64 Teqing NPT Total IR64 Teqing NPT Total
# 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
Total selected lines 47 81 215 343 652 483 530 1665
# 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
55. Screening of BC2F2 populations for
anaerobic germination
Direct seeding then submerged under 10 cm-deep water
56. Summary results of BC populations screened for anaerobic
germination and submergence tolerance
Details Anaerobic germination Submergence
IR64 Teqing NPT Total IR64 Teqing NPT Total
Total BC2F2 populations 47 47 36 130 60 57 62 179
Single plant selections per BC
population 0-5 0-6 0 - 14 0 - 15 3 - 13 0 - 12
Total selected BC2F3 lines 47 81 215 343 652 483 530 1665
Selection intensity (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93
Number of indica donors 37 38 29 104 47 50 50 147
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
Number of japonica donors 6 8 5 19 8 7 7 22
Selected lines 11 14 31 56 83 52 63 198
Selection intensity (%) 0.91 1.03 3.10 1.47 1.00 0.74 0.90 0.90
Number of intermediate donors 3 0 1 4 4 0 3 7
Selected lines 5 0 7 12 40 0 16 56
Selection intensity (%) 0.83 0.00 3.50 1.50 1.04 0.00 0.53 0.80
58. 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
Total BC2F2 populations 14 15 10 39 64 67 62 193
Single plant selections per BC
population 0 - 21 0 - 18 0 - 31 0 - 22 0 - 22 0-2
Total selected BC2F3 lines 79 77 51 207 652 255 2 909
Selection intensity (%) 5.64 5.13 5.10 5.31 10.19 3.81 0.03 4.71
Number of indica donors 1 1 0 2 49 60 49 158
Selected lines 0 3 0 3 565 221 2 788
Selection intensity (%) 0.00 3.0 0.00 1.5 11.53 3.68 0.04 4.99
Number of japonica donors 9 11 7 27 9 11 7 27
Selected lines 55 52 39 146 54 21 0 75
Selection intensity (%) 6.11 4.73 5.57 5.41 6.00 1.91 0.00 2.78
Number of intermediate donors 4 3 3 10 4 3 3 10
Selected lines 24 22 12 58 33 2 0 35
Selection intensity (%) 6.00 7.33 4.00 5.80 8.25 0.67 0.00 3.50
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.
59. Summary results of BC populations for screening
low temperature germination and BPH resistance
Low temperature germination BHP resistance
IR64 Teqing NPT Total IR64 Teqing NPT Total
# 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
Total selected lines 79 77 51 207 652 255 2 909
# 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.
60. Screening for tolerance to phosphorus
deficiency
Tested in natural conditions in Pangil, Laguna.
69. 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
70. 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.
71. 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
72. 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.
73. 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
74. 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.
79. 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
82. 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
86. 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
87. 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 %)
88. 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 donors (%) 80.5 90.3 74.3 87.8
89. 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)
90. 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.
91. 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).
92. 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.
95. 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
96. 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
97. Can we develop ILs with extreme
phenotypes for selected target
traits?
98. 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.
99. 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.
100. 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+
101. 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.
102. 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;
103. 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
104. Progeny Testing of DT ILs Under Stress
(no irrigation after transplanting)
DT C418 ILs Check (C418)
105. Progeny Testing Under Stress
(no irrigation after transplanting)
Promising DT C418 ILs
106. 2001-2002 DS BC2F4 progeny testing
IR64 ILs for quality IR64 (CK) DT IR64 ILs