Rice germplasm resources and breeding1

Rice germplasm
Ri
l
resources and breeding
d b di
Sansanee Jamjod
j
CMUPNlab
l b
Department of Plant Science and Natural Resources,
F lt f A i lt
Faculty of Agriculture, Chiang Mai University
Chi
M iU i
it
• Thailand
Thailand local rice local rice
germplasm
• Genetic diverstiy, structure y,
and dynamics
• Utilzation of local germplasm
Distribution of common wild rice ((Oryza
y rufipogon
p g Griff.)) and
center of diversity of cultivated rice (Oryza sativa L.)
Primary gene pool of O. sativa
ขาวปา
Common wild rice
ขาววัชพืช
Weedy rice, weedy form
ขาวปลูก
Crop rice, cultivated rice,
domesticated rice
Environment Diverse
Uniform
Population
l i
Genetic diversity within population
l ti
Genetic diversity between y
population
Crop rice
Wild rice
Perennial
Annual
Landrace
Pure line
Uniform
Diverse
Genetic d
diversity b
between population
p
n
Weedy rice
Weedy rice
Population
Genetic diversity within population
l ti
Natural habitats
Farmers’ field
Primary gene pool of O. sativa
ขาวปา
C
Common
wild
ild rice
i
(O. rufipogon Griff.)
Perennial common wild rice
Common wild rice ((Oryza
y rufipogon
p g Griff.))
perennial, annual, intermediate
photoperiod
h
i d response
cross-pollination
long, red awn
vegetative propagation
Oryza rufipogon
• black glume
• red pericarb
• shattering
• dormancy
Annual common wild rice
ขา วปาชนิดปเดีียว
Natural gene flow between crop rice and its wild relative
O rufipogon
O.
fi
O. sativa
O. sativa
Product of P
d t f
natural gene flow
gene flow found in farmers’ farmers’
field
Gene flow between crop rice and its wild relative
Crop rice, farmer’s seed
Crop rice
Gene flow
Gene flow
G
Gene flow
fl
Introgressive forms
Wild rice
Wild rice
Farmer selection
New local cultivars
Source of genetic Source
of genetic
variation
Introgressive forms
Common wild rice (O. rufipogon)
weedy form
weedy form
Gene flow between crop rice and its wild relative
Crop rice, farmer’s seed
Crop rice
Gene flow
Gene flow
G
Gene flow
fl
Introgressive forms
Wild rice
Wild rice
I t i hi h i
Intensive, high input, production system
t
d ti
t
Crop rice
Gene flow
Weedy rice
Introgressive forms
Weedy rice
Weedy rice
Weedy, invasive form
Weedy, invasive form
crop rice
p
Weedy rice
Weedy rice
2001 Kanchanaburi and Nakorn Nayok
North East: KDML105 fields
Year
2001
2002
2003
2004
2005
2006
2007
Area of infestation (ha)
80
320
1,600
8 000
8,000
>80,000
200 000
200,000
>300,000
Yield loss due to shattering before harvest
Rice
e yield (t/ha
a)
6
5
r = 0.917
4
3
2
1
0
20
40
60
80
Weedy rice density (%)
100
Maneechote et al. 2004 IRRN 29(2)
5
2 5
95
5
23
Wild population (42)
Weedy population (12)
cultivated rice (39
cultivated rice (
(39))
10 individuals per population
Genetic diversity: based on 12 SSR markers
Population
Genetic diversity Genetic differentiation within total within among O. rufipogon
O
rufipogon
Perennial (25)
0.635
0.815
0.180
0.221
Annual (17)
0.445 0.783 0.338 0.432
Weedy (12)
0 412
0.412 0 723
0.723 0 312
0.312
0 431
0.431 Cultivated (39)
Cu
ti ated (39)
00.000
000
00.780
80
1.000
000
Population structure
Crop
Weedy
Wild
Crop K
Crop
K=3;
3; yellow, pink, and blue
yellow pink and blue
Wild K=2; red (A) and green (P) Crop alleles escape into wild populations
C
Crop
W d
Weedy
Wild
Source: Anupong Wongtamee
WR CM
WR PC
SPR1
CNT1
N h
Northeast Wild rice NE
KDML
O rufipogon
O. rufipogon Annual
Cultivated & Weedy
Weedy
Perennial
0.05
Pusadee et al. 2012
Primary gene pool of O. sativa
ขาวปลูก
Crop rice
rice, cultivated rice,
rice
domesticated rice
RD6
KDML
HYVs
RD6
KDM
L
Bue Po Lo (>700m) Bue
Po Lo (>700m)
Bue Chomee (500‐600m)
Muey Nwang (300‐400m)
Muey Nwang (300
400m)
Bue Cho Mee
Bue Po Lo
Muey Nwang (MN)
Fst 0.22
at 5 RM markers 18 seed
l t
lots
GM infestation (%) of 5 local Muey Nawng (MN) and 3 pure line varieties tested with 3 GM accessions
Gall m
midge infestation (%))
100
MN6
80
MN5
MN16
60
MN20
MN9
40
MN62M
RD4
20
RD1
0
Tak
Chiang Mai
Ubon Ratchathani
G ll id
Gall midge accessions
i
Source: Prateep Upkaew
Local MN
Local MN
Pure line checks
Source of g
genetic variation (Local
(
rice varieties))
• Al tolerance ((Bue Bang)
g)
• Grain Fe, Zn, anthocyanin
• Gall midge resistance (MN)
Relative Root Length (RL in Al30/Al0) of Bue Bang (BB) compared with 9 improved rice varieties
9 improved varieties
80
Relative rroot length
h (%)
Sourcce: Nattin
nee Phattaarakul
BB
60
40
20
0
BB
SPR1
AUT1
PGR2
PTT1
SPR2
KDML105
CNT3
CNT1
CNT2
Breeding works
g
Grain quality
Grain
quality
Anthocyanin, Fe, Zn
Pure line selection
Pure line selection
Pedigree method
Specific characters from wild and weedy rice
Backcrossing
Improve local rice for adaptation Composite crosses
Composite crosses
Shuttle breeding
Participatory plant breeding
Participatory plant breeding
Utilisation of wild and weedy rice
Utilisation of wild and weedy rice • Traits promote outcrossing for hybrid rice industry (stigma, anther, reproductive development)
• Traits provide advantage in agronomic characters (competition, seed number)
Genotypic variation in reproductive traits
Wild rice
4.50
AAnther length (mm
m)
4.00
3 50
3.50
3.00
2.50
2.00
1.50
1 00
1.00
0.50
0.00
SKN
PSL1
PSL2
PSL3
PTT1 SPR1
CNT1
RD1
RD4
RD10
RD29
Popular rice varieties
R258 IR68144 TDK1
TDK7 WR (PC)
Genotypic variation in reproductive traits in
wild x cultivated rice
Selection
Evaluation
Backcrossing to
elite variety
Score
1
Anther
2
3
Stigma
SPR1
cultivated rice
Common wild rice
Wild rice
Selected plants in segregating populations
O rufipogon
O.
SPR1
cultivated rice
Common wild rice
Selected plants in segregating populations
O rufipogon
O.
Breeding works
g
Grain quality
Grain
quality
Anthocyanin, Fe, Zn
Pure line selection
Pure line selection
Pedigree method
Specific characters from wild and weedy rice
Backcrossing
Improve local rice for adaptation Composite crosses
Composite crosses
Shuttle breeding
Participatory plant breeding
Participatory plant breeding
Gall midge infestation of local rice in highland
หลอดบั่ว
หลอดบว
Karen,
Nonglutinous
type, gallmidge
Thung Luang (865 m)
Thai, glutinous
Intermediate
gallmidge
Mae Moot ((400
400m)
m)
CMU ((330
330))
MM
0.5
0.5
2.5
4.2
0.0
0.0
1.4
00
0.0
Gallmidge infestation (%)
at
TL
cd
1.1 d
cd
2.9 d
cd
0.0 d
bc
0.0 d
d
0.0 d
d
0.0 d
cd
6.7 cd
d
5 4 cdd
5.4
1.1
7.4
11.5
3.0
cd
b
a
cd
VVarss
MN26
MN27
MN28
MN29
MN30
MN31
MN32
MN33
Checks
MN 62M
PTT 1
SPT 1
KDML 105
22.11
14.3
23.3
11.7
d
d
a
c
IP pure line var.
HYV
HYV
IP pure line var.
X
MN30, 31
1
F1
F2
F3
1
2
2
3
3
4
4
5
5
6
6
7
7
8
8
9
9
PTT1
10
Bulk population
breeding
10
CMU
Mae Moot (MM)
Thung Luang (TL)
(330 m)
(400 m)
(865 m)
CMU
CMU
CMU
Wet season:
Adaptation, gallmidge resistant,
farmer participatory
Dry season: photoperiodinsenstivity
Thung Luang (TL)
CMU
Plant Genetic Resource and Nutrition@Chiang
l
i
d
i i @ hi
Mai University i i
i
(CMUPNlab)