improving disease resistance of maize in the developing world
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Improving disease resistance of maize in the developing world: challenges and opportunities
Santiago Mideros17 February 2011CIMMYT
WFP/Elmer Martinez
OutlineChallenges and Opportunities
◦General
◦Specific Aflatoxins
AFB1
OpportunitiesAg. development is back
Science & Technology◦Genetics, genomics, plant immunity◦Precise phenotype, barcoding, databases
CIMMYT◦Germplasm◦World network◦Mandate
ChallengesClimate Change
◦Food security◦Maize pathology
New or emerging pathogens/races◦Movement of germplasm◦Change on cultural practices
Food quality, health concerns, mycotoxins
Science ImpactPolicy
Climate Change
Uncertainty in predictions
Lack of historical dataFusarium species and
DON
Battisti and Naylor 2009
New and (re)emerging pathogens or racesGray Leaf Spot
◦ Cercospora zeina◦ Cercospora zeae-maydis
Maize fine streak virusMaize streak
(gemini)virusPhaeosphaeria leaf spot
Maize streak virus Shepherd et al (2010)
Policy
Investment on science in developing countries
Aid and technology from developed countries◦ Budgetary concerns
OpportunitiesAg. development is back
Science & Technology◦Genetics, genomics, plant immunity◦Precise phenotype, barcoding, databases
CIMMYT◦Germplasm◦World network◦Mandate
OpportunitiesAg. development is back
Science & Technology◦Genetics, genomics, plant immunity◦Precise phenotype, barcoding, databases
CIMMYT◦Germplasm◦World network◦Mandate
ScienceAssociation Mapping Yan et al, 2011
◦Northern Leaf Blight, ◦Southern Leaf Blight, ◦Gray Leaf SpotWisser, Kolkman, Benson, Nelson, Balint-Kurti (in review)
Glutatione S-transferase
Nested Association MappingSouthern leaf blight (Kump et al, 2011)
32 QTL51 SNP: Receptor like kinases, Glutathione S-
transferase
Northern leaf blight (Poland et al, in review)
21 QTL60 SNP:
◦ Receptor like kinases ◦ Ethylene response factor ◦ Mlo-like
Quantitative disease resistance PTI (Basal Resistance)
Gray leaf spot (Benson et al, in preparation)
12 QTL21 SNP
Science (cont.)Mutant-Assisted Gene Identification and
Characterization (MAGIC)
• Fine mapping genes responsible for resistance in maize
Nature Biotechnology Volume: 28, Pages: 365–369 Year published: (2010) DOI: doi:10.1038/nbt.1613
Technology
OthersCommunication (Internet)
◦Developing partnerships◦Collaboration◦Capacity building
Genomic selectionGenotyping by sequencing
◦Next generation sequencing
OpportunitiesAg. development is back
Science & Technology◦Genetics, genomics, plant immunity◦Precise phenotype, barcoding, databases
CIMMYT◦Germplasm◦World network◦Mandate
Germplasm
Photo by Suketoshi Taba, Yan et al 2011
Multiple Locations
Partners
National agricultural research institutes
Other international organizations
Universities in developing countries
Universities in developed countries
Private companiesNGOs
Sustainable Disease Management
Disease resistanceNo silver bullets
◦Deployment: Pyramids Refuge areas (Bt)
Resistance + management
Multiple disease resistance
Effect of a single QTL. Chung et al, 2010
OutlineChallenges and Opportunities
◦General
◦Specific Aflatoxins
AFB1
Challenges and OpportunitiesA practical example
Challenge:Mycotoxin contamination
Opportunities:Technology and geneticsFood systems
Mycotoxins
AflatoxinsA. flavus and A. parasiticus
aflatoxinsPotent hepatocarcinogenAcute: death; liver damageChronic:
◦ Immune suppression, growth impairment
◦ Hepatocellular carcinomaFinancial burden
AFB1
Other Ear RotsGibberella Ear RotFusarium graminearumDeoxynivalenol = DON = Vomitoxin
Fusarium Ear RotFusarium verticillioidesFumonisin
Photo: A. Robertson
Aflatoxin child stunting
Regulation & Exposure
1ppb = 1 ng per g or 1mg per metric ton
Country Consumption
(g/p/day)
Max. aflatoxin
(ppb)
Exposure(ng/bw/
day)
Western Europe
33 4 0.3 – 1.3
USA 86 20 0.26
Southern Europe
148 4 0 - 4
Kenya 248 20* 3.4 - 133
Mexico 300 20 14 - 85
Sources:Liu, Y. and Wu, F. 2010. EHP. 118: 818-824
Reddy et al. 2010. Toxin Reviews. 29: 3-26
2010 aflatoxin outbreak, Eastern Province, Kenya
Survey in western Kenya 09
Source of maize N % >10 ppb
% >20 ppb
Gifts from friends or relatives
30 27 7
Purchased 349
11 2
Own-grown 183
5 2
Food aid 7 14 0Total 56
914 3
S. Mutiga; V. Hoffman; and R.J. Nelson unpb
Strategy
Components of resistanceTissue specificComponents of
resistance◦ Latent period (LP)◦ Sporulation
intensity (SP)◦ Infection
frequency (IF)Colonization
◦ qPCR
CML69 Sc212m
Mp339 Tx303
Picture: K. Loeffler
qPCR Development
A. flavus Primers:◦Internal Transcribed Spacer 1 (ITS1),
5.8S rDNA, and ITS2◦Genbank
A. flavus, A. oryzae, A. parasiticus, A. sojae, A. tamarii, Emericella nidulans
A. flavus biomass in maize is strongly correlated with aflatoxin concentration
0
1
2
3
4
Infe
ctio
n
Coe
ffici
ent (
log
IC)
2 3 4 5 6 7 8
Aflatoxin (log ng/g)
Correlation between infection coefficient (IC) and aflatoxin = 0.85 **
Pedigree/Line IC ng/gCML103 0.78 a 1.18 10.03 a 22735Mo17 0.62 ab 0.85 9.39 ab 11982B73 0.51 abc 0.67 9.54 ab 13917B97 0.33 bcd 0.39 9.22 abc 10118MS71 0.28 bcd 0.33 8.21 abcde 3689Oh43 0.27 bcd 0.31 7.84 bcde 2542Oh7B 0.21 cd 0.23 8.16 abcde 3483IBM54 0.11 d 0.12 7.93 bcde 2790NC358 0.11 d 0.11 6.75 defg 854IBM262 0.09 d 0.10 8.75 abcd 6283Ky21 0.08 d 0.08 6.96 defg 1056Tx303 0.06 d 0.06 7.20 cdef 1333Ki3 0.05 d 0.06 7.46 bcde 1739Mp339 0.05 d 0.05 6.79 defg 886M37W 0.02 d 0.02 6.43 efgh 622CML52 0.00 d 0.00 4.55 h 94Mp313E 0.00 d 0.00 4.84 gh 126CML247 0.00 d 0.00 5.15 fgh 172
A. flavus Aflatoxinlog (IC+1) log (ng/g+1)
Mideros et al 2009 Plant Disease 93: 1163
ExperimentsNew York Mississippi
Components of resistance for diverse inbreds: 3 years of studies (P-values)
Component of resistance
Maize Tissue
SilkDeveloping
KernelMature Kernel
In-vitro
Latent Period0.062
4 nsInfection Frequency
0.0018 ns
Sporulation0.006
7 0.0963Colonization (qPCR) - 0.2097
FieldColonization (qPCR)
0.0312 - 0.0301
Aflatoxin - - 0.0006While
significant, not correlated with
aflatoxin
Kernel resistance correlations
Field In-vitro Flint-Garcia's traits
Colonization (qPCR)
Colonizatio
n (qPCR
)
Sporulation Mois
tureProtein Fat Fiber Ash
Carbhdrt
sd wgh
t
%endspr
m
Field Aflatoxin 0.70*** 0.02 0.06 -0.03 -0.45 -0.25 -0.68** -0.57* 0.52* 0.57* 0.12
Colonization -0.16 -0.01 -0.02 -0.21 -0.17 -0.47 -0.50 0.27 0.46 0.09
In-vitro Colonization 0.00 0.33 -0.38 0.03 -0.07 0.03 0.23 0.14 -0.05
Sporulation -0.53* 0.39 0.27 0.03 0.26 -0.38 -0.41 0.15
Strategy
Model selection QTL mapping (B73 x CML322)
Sporulation SPLatent Period LPInfection Freq IF
Trait Year Marker Position source
DvK Sporulation 2007 m758 6.07 1.8E-03 B73
DvK Sporulation 2008 m758 6.07 3.7E-05 * B73
DvK Sporulation 2008 m838 7.06 7.8E-05 * B73
DvK Sporulation 2008 m209 2.03 1.0E-04 * CML322
Aflatoxin, MS 2008 m500 4.08 4.4E-06 ** CML322
Aflatoxin, MS 2008 m746 6.06 7.0E-05 * CML322
Aflatoxin, MS 2008 m35 1.03 2.2E-04 * CML322
Silk LP, NY 2008 m316 3.04 2.1E-10 ** CML322
Silk LP, NY 2008 m421 3.09 7.1E-10 ** B73
Silk LP, NY 2008 m540 4.10 2.6E-08 ** CML322
Silk LP, NY 2008 m154 1.11 2.7E-07 ** CML322
Silk LP, NY 2008 m706 6.03 1.0E-06 ** B73
Silk LP, NY 2008 m849 8.01 2.6E-06 ** B73
Silk LP, NY 2008 m168 1.11 1.3E-04 * B73
Silk LP, NY 2008 m857 8.03 1.6E-04 * CML322
Silk SP, NY 2008 m911 8.06 2.1E-08 ** CML322
Silk SP, NY 2008 m766 7.01 3.7E-08 ** B73
Silk SP, NY 2008 m428 3.09 1.0E-06 ** CML322
Silk SP, NY 2008 m763 7.01 4.9E-04 * CML322
Silk IC, MS 2008 m774 7.02 4.4E-05 ** B73
Silk IC, MS 2008 m775 7.02 5.0E-06 ** CML322
Aflatoxin, MS 2009 m821 7.04 1.0E-07 ** B73Aflatoxin, MS 2009 m1096 10.07 1.0E-07 ** CML322Aflatoxin, MS 2009 m216 2.03 9.3E-05 * CML322Aflatoxin, MS 2009 m746 6.06 2.7E-03 CML322
p-value
25 QTL
QTL studiesPlant
DiseaseGermplas
mSource
Aspergillus Ear Rot
Mp313E x Va35
Wilcox et al. (unpublished)
Mp313E x B73 Brooks et al. 2005
Mp717 x Nc300
Warburton et al. 2009
Mp715 x T173 Warburton et al. 2010
CML322 x B73 Mideros et al. (unpublished)
Gibberella Ear Rot
CO387 x CG62 Ali et al. 2005
Fusarium Ear Rot 3 x 18 Perez-Brito et al. 2001
5 x 18 Perez-Brito et al. 2001
87-1 x Zone3 Ding et al. 2008
GE440 x FR1064
Robertson-Hoyt et al. 2006
NC300 x B104 Robertson-Hoyt et al. 2006
9.029.03
9.04
9.06
9.07
9.08
9
9.01
bnlg1209
9.05
umc1191umc1033
phi027
umc2121
umc1789
bnlg128
umc1277
umc1654
bnlg1191
umc1688
umc1867umc1291
10.00
bnlg1451
10.01
bnlg640
10.02
umc124610.03
umc1053umc1506
10.04
umc1477
10.05
umc1084
10.07
bnlg1450
10.08bnlg1185
10
umc1898
phi062
10.06 umc1061
5.00
5.02
5.04
5.03
5.01
5.09
5
5.06
bnlg1046
umc1761
mmc0081
umc2019mmc0481
bnlg1306
umc1153
bnlg603
5.05
5.07
5.08 umc2136bnlg2291
umc1667
umc10084.00
umc16824.01
nc004
4.03
nc005
bnlg1137
4.05
bnlg2162
4.06
umc1051
4.07
umc1173
4.08
umc1631
umc2011
4
umc17574.02
4.04
sts001
bnlg1126
4.09
4.10
2.06
2.07
2.08
2.00
2.01
2.03
2.04
2
umc1065
umc1079
phi109642
umc11852.02
umc1783
umc1637
umc1526
2.05
bnlg371
bnlg371
umc12921.00
umc17271.01
umc1166bnlg14291.02umc1070
phi001
1.03
umc1590bnlg1057
1.06
umc1035
1
umc1065
umc2047
1.09
umc14211.11
umc1630
umc11181.12
bnlg1596
bnlg400
1.07
1.08
1.10
bnlg15981.04
1.05
umc2170
bnlg1759
phi0756.00 bnlg238
6.01
umc1006
6.03
umc10146.04
bnlg1702
6.05
6
bnlg1165
6.02
umc1463
6.06
umc1248
6.07
phi0896.08umc2059
6.09 umc1127
bnlg1154
umc1498
umc1632
umc21053.00umc1746
3.02
umc1970
3.03 bnlg1144
3.04
bnlg1325
3.05
phi036
3.06
phi029
3.07
bnlg1063
3.08
bnlg1350
3.09
bnlg197
3.10
bnlg1182
3
umc1361
umc2048
umc1062
umc1642
3.01
umc1066
7.00
bnlg1200
7.01
bnlg1070
7.02
umc10017.04
umc1029
7
phi2604857.05
umc1407
phi1167.06umc1799
umc2222
umc1978
phi1147.03
umc11398.00
bnlg1194
8.01
bnlg1352
8.02
bnlg1863
8.03
bnlg666
8.04
umc11498.05
bnlg240
dupssr148.09
8
bnlg1828
8.07
bnlg1350
umc19978.06
8.08
Mp313EaMp313EbMp717Mp715Oh516Tex6B73CML322
Collaboration with M. Warburton
QTL Meta-analysis
Consensus Genetic Map
Projection of QTL and CI
Position of metaQTL
Veyrieras et al. 2007 BMC Bioinformatics 8Truntzler et al. 2010 TAG 114
Consensus Genetic Map
Consensus
Mp313E x B73
Genetic 2008B73 x
CML322
QTL Meta-analysis
Consensus Genetic Map
Projection of QTL and CI
Position of metaQTL
Goffinet et al. 2000 Genetics 155Veyrieras et al. 2007 BMC Bioinformatics 8Truntzler et al. 2010 TAG 114
1 2 43 5
6 10
97 8Aspergillus Ear Rot
AflatoxinFusarium Ear Rot
FumonisinEar rot (w)Ear rot
Gibberella Ear RotSilk disease severityKernel disease severity
QTL Meta-analysisConsensus Genetic Map
Projection of QTL and CI
Position of metaQTL
Goffinet et al. 2000 Genetics 155Veyrieras et al. 2007 BMC Bioinformatics 8Truntzler et al. 2010 TAG 114
1.012.5 Mb
1.0623.2 Mb
Sustainable Disease Management
Disease resistanceResistance +
managementEffect of a single QTL Chung et al, 2010Pre-
harvest resistance
Drought tolerance
Better varieties
Yield
Field managem
ent
Biological control
Post-harvest
management
•Resistance•Storage•Testing•Detoxification
Lower aflatoxi
ns
Acknowledgments Rebecca Nelson Tiffany Jamann Paola Zuluaga Margaret Smith Jaci Benson Bill Holdsworth Jose Luis Zambrano
R. Nelson Labo Chia-Lin Chungo Jesse Polando Samuel Mutigao Judy Kolkmano Wenzhe Lio Chris Mancusoo Nelson Chepkwonyo Ariel Fialkoo Oliver Otto Sara Heinzo Lin-Si Hsieho Kristen Kennedy o Kerri Lyons o Joy Longfellowo Ellie Walsh
Marilyn Warburton Gary Windham Paul Williams
o Gregory Flinto Ladonna Owenso Mike Alpeo Victoria Scott