arm 2007: dissection, characterisation and utilisation of disease qtl -- r nelson
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Indonesia- Bustamam
- Utut
IRRI- Vera Cruz
- Leung- Brar
CSU- Leach
KARI- Gethi
Cornell- Nelson- Smith
NCSU- Balint-Kurti
Rice Maize
Generation Challenge Program
Project #8Update 2007
Dissection, characterization and utilization of disease QTL
Synthesis maps (Complementary) mechanisms Insight on MDR
Understanding the trait
Germplasm panel: resistance sources
Stress resistant varieties
(Actionable) insightsre: breeding populations
Improving the trait
dQTLdiscovery dQTL genes
Dissecting the trait
dQTL vs.expressiondQTL NILs
PublishedNILs;
Histopathology Diversity panel;RS populations
Mapping populations
Disease panelAssociation panel
Diallel
Selection from diallel
Selection from AB-QTL populations
(poster 3.25)
Linkage mapping Selection mappingAB-QTL mappingMutant analysis
Multiple strategies
(poster 2.9)
Deletion analysisQTL dissection
Assocation mappingNAM
Array studies
GR6458GR6489GR6603GR6686
GR7534
GR6728GR6989
Chip-analysis of loss-of-resistance mutants
J. Leach, G. Diaz, and M. Bruce, CSU
spl1
LOC_Os01g27150 LOC_Os03g56800
LOC_Os04g54240
IR64
IR64
IR64
GR
6686
GR
6603
GR
6603
GR
7534
GR
6728
GR
6686
LOC_Os01g64720G
R66
03
GR
6686
GR
6728
GR
7534
IR64
LOC_Os01g67720
GR
6603
GR
6686
GR
6728
GR
6989
IR64
GR
7534
Allelic series of deletion mutants
Gene model position on chromosome 12
Rat
io o
f sig
nific
ant p
robe
s in
pro
be s
et
Mutant line
All mutants show spl1 phenotype.
Two had been confirmed as allelic by complementation tests
OXLP cluster
Oxalate oxidase (germin-like protein)
R2 = 0.7039P = <0.001
0.0
0.5
1.0
1.5
2.0
0 2 4 6 8Rice blast disease ratingR
elat
ive
expr
essi
on T
0/W
T
Rice blast disease rating
More More silencingsilencing
Carillo and Vera Cruz, IRRI
RNAi
Manosalva and Leach, CSU
Increased silencing of Chr. 8 OsGLPgenes in T0 rice correlates with increased disease
u1228 m0371
Chromosome 4
p072u1008b1434
nc135
u1669 u1509 b1126u2281
p096 b1265u2054u1142
u1451u1896 u2027
u2038b1189u1808
u2041m0321u2285
u1313u1999 u1101
b589b1890
0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700
Chromosome 1
Chromosome 2
p96100u2246 u2363
b1017b1338
m0111
u1756u1261
u2248p109642
b1018 m0401b1831b1036b1138u1080u2372b1329
u1042 b1662 b1940b1520u1252
p101049u1696
AY111236
0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700
Chromosome 3
u2118u2256
p104127u1886b1325b1523u1057
u2258u2369
p099u2000u2158b2047
u2261 u2264u1773
b1456b1904u1920u2376
u1266b1449
b1047u2266 u2269
u2270u2271
dupssr17
b1605 u1825 m0251b1108u1273u2276
dupssr33b1182b1496
u1062u1594u1136
0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800
Chromosome 5
u1308 u1496 u1781 b105b1046 u1447 u1355
b1287b1208
m0081 u1853 u1722 p101u2216
p048b2305
b118 AY105910u2307
0.0 50 100 150 200 250 300 350 400 450 500 550 600 650
Chromosome 10
p041u1293u1291 u1152
u2034
u1337p059
u1863u1866
p050u1995b1526u1077
u1115 u1506 b1028 u1084b1360
b1185
50 100 150 200 250 300 350 400 4500.0
b1065
Chromosome 8
u1414 b1194 u1913 b1834 b1863 u1457 b1176 b666 b1782 b1031 dupssr14 b1056 b1131
0.0 50 100 150 200 250 300 350 400 450 500 550 600
Chromosome 6
b1043 b426b1371
u1083u1572
AY111964
m0241 b1732u1859
p299852 b1740 b1521
b1538
nc009u2324
0.0 50 100 150 200 250 300 350 400 450 500
Chromosome 7
b1367b2132 u1159 b1094 u1983 b1022
b1808b1305
b1070b1805 b1666 b2259 b1407 p051
0.0 50 100 150 200 250 300 350 400 450 500 550 600
Chromosome 98000.0 50 100 150 200 250 300 350 400 450 500 550-39.0 700 750600 650
u1279 b1724u1867u2393
b1810b1583u2335u1596
u1430
b244 p061u1107u2398u1120u1078
u1231u2095u2343u2371
b1191u1366
b619b128
u1982 u1277
NC250 Introgression likely derived from B37
NC250 Introgression likely derived from
Nigerian Composite ARb
NC250 Introgression in both NC292 and NC330
NC250 Introgression in NC292
NC250 Introgression in NC330
Unknown no SSR data
Unknown bands present in NC292 and NC330 not present in
B73 or NC250
Unknown bands present NC330 not present in B73 or NC250, NC292
has B73 bandMajor SLB QTL positions B73/NC250A F2:3 population
umc1704
umc1532umc2011bnlg1917
u1636 dupssr19
b2228
u1177b149
0.0 50
a31 b1429u1160 b1484
b1866b652
u2227
b2086u1297
u1988u1254u1035 u1122
u1661u1358b1556
b1025u1128
p037u1848
m0041
u2047u1298
u1431b1671b1347
u1500p2654
54
u1553u1129u1118 b2123
u1725u2244
100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100
u2053 u1576
b594IDP1471IDP4016
500
BBCC
GG
FFEE
DD
II
JJ
HH
AA
Introgression C
Introgression F
Introgression G
Introgression J
B73
NC292Introgression B
Introgression D
Zwonitzer and Balint-Kurti
Increase in rate of lesion development
0.07
0.075
0.08
0.085
0.09
0.095
B73 Het SEL*
Incu
batio
n Pe
riod
-1Antagonistic reactions for NLB and rust resistance
0
10
20
30
40
50
60
B73 Het SEL*
DLA
Decrease in rust severity
R
S
R
S
Selected allele
NLB
p < 0.001
Rust
p = 0.01
J.A. Poland and R.J. Nelson, Cornell
Chung and Nelson
Incidence of E. turcicum growing into thexylem on different maize genotypes
(7 days after inoculation)
0
20
40
60
80
100
CML52 Tx303 B73 TBBC3_42
Maize genotype
% o
f inf
ectio
n si
tes
hyphae in the xylem
0
10
20
30
40
50
60
70
80
90
100
110
IF
Ki3
M16
2W 20 60 25 11C
ML6
920
1C
ML3
22B
73 128
173 78 17 121 9
127
119
Ky2
1 48 42 81M
37W 26
CM
L322
-Inoc 192
194
185
137
Tx30
3 79 90 615
4 66 50 166 19 68
CM
L322
-Moc
kO
h7B
Line
Infe
ctio
n Fr
eque
ncy
(%)
Maize + drought = aflatoxicosis
Mideros and Nelson, Cornell
Resistance to infection by Aspergillus flavus
Chr 2 Chr 3 Chr 5 Chr 7
Panicle weight Leaf blast Lesion number
Diseased leaf areaHarvest index Height
Grain filling
Mapping of QTLs for resistance to blast and drought tolerance in rice
Vandana / Moroberekan derivatives; IRRI & India
Datasets and lines:Advanced rice genotypes with drought and blast resistance
Moroberekan / Vandana(India-IRRI)
Oryzica llanos 5 / Way Rarem(Indonesia / IRRI)
Genetics + breedingParent 1&2 CML
312CML 384
TZMi 102
TZMi 711
TZMi 712
CML 204
CML 373
CML 312 Self
CML 384 Self
TZMi 102 Self
TZMi 711 Self
TZMi 712 Self
CML 204 Self
CML 373 Self
Moderate x Moderate
CML 312 x TZMi 712
• Diallel study of GLS resistance
• F2:3 and BC4F4 lines pending
• Promising hybrids identified
Gene(s)
QDR-QTL
QTL Dissection
NILs
Nested Association
Mapping
Associationmapping
RIL populations
Selection mapping
Targeted HIF extraction
Introgressionlibraries
Deletion mutants
Varieties
Affymetrixdata on
deletion mutants
5 SLB datasets4 GLS datasets 3 NLB datasets
2 SLB datasets2 NLB datasets2 smut datasets
(collab with Buckler / Holland)
Materials, marker data and
pheno data