1. Indonesia
- Bustamam
- Utut
KARI
- Gethi
Cornell
Dissection,
characterization
and utilization
of disease QTL
IRRI
- Vera Cruz
- Leung
- Brar
CSU
- Leach
- Nelson
- Smith
NCSU
- Balint-Kurti
Rice Maize
Generation Challenge
Program
Project #8
Update 2008

2. 5 6 7 8 9
10
9
8
7
6
5
Gray Leaf Spot E-MBLUP
Northern Leaf Blight E-MBLUP
disease GLS NLB
SLB ***0.61 ***0.62
GLS - ***0.45
SLB
a: Unknown gene
b: tasselseed2
c: Glutathione S-Transferase
4
GLS
NLB
3
2
1
Randy Wisser
1 2 3 4 5 6 7 8 9
1 2 3 4
0
Southern Leaf Blight E-MBLUP
E
E
Association mapping
population (Buckler;
n=~300): 11 datasets
for three diseases
-0.4 -0.2 0.0 0.2 0.4 0.6 0.8 1.0
allele effect
a
b
c
{
{
{

3. QTL identified in NAM for NLB , SLB and GLS
0 QTL identified in NAM for NLB , SLB and GLS
-1
-2
-3
-4
-5
Nested association
mapping population
(Buckler et al.; n=5,000):
6 datasets for 3 diseases
FLECKS
-6
-7
-8
-9
-10
SLB
NLB
GLS
12 of 13 NLB-QTL in full NAM
analysis are present both years
K. Kump/PBK et al., NCSU; J. Poland and J. Benson/RJN et al., CU

4. 9
8
7
6
5
AUDPC
Gray Leaf Spot: Allele effects at qCz4.06
6 alleles?
24
22
20
18
16
14
12
10
8
6
4
LSmean Diseased Leaf Area
(%)
Northern Leaf Blight: Allele effects at qEt8.06
Parental Allele
3 alleles?

5. Near-isogenic lines
Crop/lab Developer Source Background Target No.
lines
Rice / HL, JL Leung, Leac
h
Deletion library IR64 Whole
genome
n=12
char.
Rice / HL Leung SH2-2 TX2-13 (HIF) Chr. 6, 9 n=13
Rice /
Bustamam,
OL5 Way Rarem Chr. 6, 9 n=2
CMVC, MB
Vera Cruz
RRiiccee // CCMMVVCC MMoorroobbrrkknn VVaannddaannaa nn==77 nn==6600
Maize / PBK Zwonitzer NC250 B73 n=12 n=137
Maize / RJN Chung Tx303 B73 1.02,
1.06
n=17
Maize / RJN Chung CML52 B73 (HIF) n=9 n=46
Maize / RJN Chung DK888 S11 (HIF) n=5 n=23
Maize / JG Gethi TZMi102, TZMi711,
TZMi712, CML384,
CML312.
CML 204, CML
373 (HIF)
Whole
genome
n=72

6. NLB:
histopathology
Field
Infection efficiency (2 days after inoculation)
0
0.2
0.4
0.6
0.8
1
Tx3 03
B73
Maize genotype
TBBC3_38_05F
T BBC 3_42 _10E _2
I n f e c ti o n e ffi c i e n c y
(s u c c e s s f u l in f e c t io n /
g e rm in a t e d c o n id ia )
Tx303 allele at the NLB QTL
in bin 1.06
QTL x E
reduces fungal penetration
SLB: Field
Growth Chamber
Incidence of E. turcicum growing into the xylem
(4 days after inoculation)
0
0.1
0.2
0.3
0.4
0.5
0.6
Tx303
B73
Maize genotype
TBBC3_38_05F
TBBC3_42_10E_2
Incidence
(hyphae in xylem / infection site)
B73 allele at the NLB QTL in
bin 1.02
More robust relative to
reduces fungal colonization
environments?
of the vasculature

7. QTL isolines with impressive phenotypic effects
in the field
+ QTL – chr. 6 - QTL – chr. 6 + QTL – 1.02 - QTL – 1.02

8. A. flavus biomass estimated by
Quantitative Real-Time PCR is
strongly correlated with aflatoxin
concentration
4
3
2
1
0
log Infection Coefficient
2 3 4 5 6 7 8
log (ppb+1)
A. flavus Infection Coefficient (log IC)
Aflatoxin Concentration (log ppb)
Pearson correlation == 00..8855**** nn==2200
QTL mapping for
silk and young
kernel resistance
to colonization
• CML322 x B73 RILs
• Tx303 NILs (B73 background)
Bin 7.02-7.03
• CML52 HIFs (B73) Bin 6.05
To be confirmed with 2008 field data (analysis in progress) S. Mideros, Cornell

9. MDR varieties in release process in Kenya
Test Code Pedigree Region Tons Ha-1
MTPEH200805 TZMi 712/CML 373//CML 312 Coastal lowlands 7.0
KATEH200804 TZMi 102/CML 373//CML 312 Drylands 9.6
MTPEH200801 CML 373/TZMi 711//CML 312 Coastal lowlands 8.9
KATEH200803 CML 373/TZMi 711//CML 312 Drylands 9.3
MTPEH200803 CML 373/TZMi 102//CML 312 Coastal lowlands 7.6
MTPEH200802 CML 204/TZMi 711//CML 312 Coastal lowlands 8.8
MTPEH200804 CML 204/TZMi 102//CML 312 Coastal lowlands 7.1
KATEH200802 CML 204/TZMi 102//CML 312 Drylands 9.6
KATEH200801 CML 204/CML 373//CML 312 Drylands 10.0
J. Gethi, KARI

10. Vandana/Moroberekan-derived BC3F8 intermated lines for multilocation
trials in India, 2008
NAME Yield (g) Yield (g)
Seedling
blast
(0-9)
% DLA
PBS
(0-9)
Neckblast
(%)
Seedling
blast
(0-9)
Candidate
Gene(s)
Almora
IRRI
IRRI
(50DAS) IRRI
Almora
Cavinti
Hazaribag
Grain
Length
Grain
Shape
Grain Quality
Analysis
Chalkiness
(0-none, 9-large)
Gelatinization
Temperature
Amylose
Content (%)
Aroma
IR78221-19-3-196-B-B
(Susceptible control)
100
5.0 85.0 4.0 57.5 8.25 10.0 4.0 CHI 5 5 9 HI/I 24.5 slight
90
IR78221-19-4-54-B-B 152.5 68.5 1.0 1.5 3.55 51.3 2.0
CHI,OXO
THAU7, POX
OXLP
3 1 9 HI/I 25.4 slight
80
IR78221-19-6-7-B-B 153.5 90.4 1.0 1.0 3.25 20.8 1.0
OXO, HSP90
POX
3 1 9 I 24.7 none
70
Mean % diseased leaf area
IR78221-19-6-33-B-B 105.0 94.8 1.0 2.0 3.95 2.4 1.5
OXO, POX
OXLP
60
50
40
30
20
10
chitinase, oxalate
oxidase, thaumatin,
peroxidase, oxalate
oxidase-like protein oxalate
Traits of the advanced elite lines:
• blast resistance based on early generation multi-location testing
• morpho-agronomic traits comparable to Vandana
• presence of candidate genes associated with blast resistance
• yield comparable to Vandana under low rainfall during reproductive stage
5 5 1 I 25.5 none
IR78221-19-6-56-B-B 80.0 134.8 1.0 1.0 3.1 1.3 1.5
CHI, OXO
HSP90, POX
3 1 9 I 25.3 none
IR78221-19-6-82-B-B 165.0 70.0 1.0 1.0 3.4 7.5 1.0
OXO, POX
OXLP, PR10
3 1 5 I 25.6 none
IR78221-19-6-90-B-B 112.5 108.5 1.0 1.0 3.0 5.0 4.0
OXO, POX
OXLP
3 1 0 I 25.2 slight
IR78221-19-6-99-B-B 170.0 109.5 1.0 1.0 3.3 10.2 1.5 OXO 3 1 1 I 24.8 none
IR78222-20-7-148-2-B 70.0 128.5 4.0 1.5 5.15 3.0 0.0
CHI, OXO
OXLP, DHAP
5 5 5 HI/I 20.2 slight
0
196 54 7 33 56 82 90 99 2 IR64
BC3F8 VxM intermated lines*
oxidase

11. Deliverables over project lifetime
• Understanding the trait
• Dissecting the trait
– QTL syntheses: published
– Selection mapping: published
– Deletion mapping by dot-blot &
microarray: pub. & submitted
– Large-scale QTL analyses
• SLB, NLB and GLS
– Sets of QTL NILs (maize, rice)
– Deletions in 14 rice mutants
– Association analysis for MDR: in mapped
preparation
– Phylogenomics of candidate genes
– Win-win and win-lose QTL
• Improving the trait
– QTL characterization
– Histopathology
– Fine-mapping in progress for
several QTL in maize
– Maize lines with MDR in advanced trials in Kenya
– Disease resistant elite rice lines in India and
Indonesia