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qEt8.06 DK888. QTL region identified in F 7. umc1997. umc2210. umc1828. umc2356. umc2361. umc2199. umc1287. umc1149. umc1728. umc2395. bnlg1724. umc1777. umc1316. 110. 115. 145. 120. 125. 130. 135. bnlg240. 150. 155. umc1846. umc1121. umc2378. umc1712. umc2210. - PowerPoint PPT Presentation
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Characterization of qEt8.06 using near-isogenic line (NIL) pairsnear-isogenic line (NIL) pairsTo be able to analyze qEt8.06 in detail, NIL pairs contrasting for the 8.06 region were developed using heterogeneous inbred family (HIF) strategy (2). In HIF analysis, intermediate materials from breeding programs are used to develop NIL pairs that are isogenic at the majority of loci, but differ at a specific QTL. In order to capture alleles contributing broad-spectrum resistance in NIL pairs, we chose to start from F6 families derived from DK888 x S11. DK888 is a tropical genotype with superior resistance to multiple diseases.
Conclusions1. Consistent detection of qEt8.06 in diverse mapping
populations indicates that it accounts for a large proportion of NLB resistance in maize germplasm.
2. High-resolution nested association mapping and break-point analysis using NIL pairs has localized qEt8.06 to an overlapping region of < 4 Mb (142.9 – 146.5 Mb on physical map). The tightly linked marker umc2210 can be applied for marker-assisted selection in maize breeding.
3. Race-specificity, map position and gene action of resistance suggested that qEt8.06 can be Ht2, Htn1 or a novel resistance locus. Concurrent work of fine-mapping Htn1 locus using F2 populations derived from B68Htn1 x B68 will resolve this question.
4. The enrichment of disease QTL in the 8.06 region and its genetic complexity implies the possibility that instead of a single major gene, qEt8.06 may consist of a cluster of resistance genes. Different levels and phenotypes of resistance can be due to various combinations of alleles for multiple genes, and their expression modified by genetic backgrounds and environmental conditions. The hypothesis will be further tested through map-based positional cloning.Acknowledgements
Stephen Kresovich Institute for Genomic Diversity, Cornell UniversityMargaret Smith Dept. of Plant Breeding and Genetics, Cornell UniversityFunding from Ministry of Education, Taiwan; the Generation Challenge Program; and The McKnight Foundation.
Genetic Dissection of Loci Conditioning Disease Resistance in Maize Bin 8.06Chia-Lin Chung 1*; Jesse Poland 1*; Randall Wisser 2; Judith Kolkman 1; The Maize Diversity Project 1,2,3,4,5,6,7; Rebecca Nelson 1
1 Cornell University, Ithaca, NY; 2 USDA-Agricultural Research Service; 3 Cold Spring Harbor Laboratory, NY; 4 University of California-Irvine; 5 North Carolina State University, Raleigh, NC; 6 University of Missouri, Columbia, MO; 7 University of Wisconsin, Madison, WI; * Joint first authors
Student's t-testDK888 S11 (P-value)
Northern Incubation period days after inoculation 17.4 ± 1.7 10.0 ± 0.3 < 0.0001 ***
leaf blight (NLB) Primary diseased leaf area % 9.0 ± 4.1 65.0 ± 6.2 < 0.0001 ***
Southern Lesion length mm 1.2 ± 0.05 1.2 ± 0.06 0.719
leaf blight (SLB) Primary diseased leaf area % 29.5 ± 1.0 30.0 ± 1.5 0.585
Anthracnose Incubation period days after inoculation 7.7 ± 0.2 7.8 ± 0.4 0.698
leaf blight (ALB) Latent period days after inoculation 10.4 ± 0.7 10.4 ± 0.7 1.000
Primary diseased leaf area % 39.1 ± 12.1 38.6 ± 14.7 0.963
Anthracnose stalk rot (ASR)
Discolored internode tissueTotal % of internode 1 to 8
121.7 ± 12.9 120.0 ± 23.0 0.901
Rust First postule appearance days after inoculation 7.5 ± 0 7.5 ± 0 1.000
Number of pustules # pustules 96.0 ± 64.0 149.5 ± 37.7 0.706
Primary diseased leaf area % 14.4 ± 3.1 15.0 ± 2.7 0.790
Smut Volume of gall cm3 273.8 ± 157.4 167.5 ± 99.1 0.258
Weight of gall grams 127.4 ± 68.5 78.9 ± 46.1 0.247
Stewart's wilt Primary diseased leaf area % 72.5 72.5 –
Disease Parameter UnitAllele(s) at qEt8.06
The sixth segment of maize chromosome 8 (bin 8.06) is known to be associated with resistance to NLB and several other diseases (4). Two qualitative resistance loci (Ht2 and Htn1) and several QTLs for NLB resistance have been localized to this region. In response to a recurrent selection program for NLB resistance, significant changes in allele frequencies provided evidence of selection acting at several loci in bin 8.06. One of the putatively selected allele has been validated in F2 families derived from the selection mapping population (5). To dissect the complex region, and to understand the relationship between qualitative and quantitative disease resistance in maize, a set of genetic stocks capturing a range of resistance alleles at bin 8.06 has been used for QTL mapping and characterization.
Maize disease QTL consensus map(Wisser et al., 2006)Chromosome 8
Erwinia wilt Viral
diseases
Aspergillus flavusEar rot and stalk rotCommon
smutDowny mildewCommon
rustSouthern rustGray leaf
spotSouthern leaf blightNorthern leaf blight
Disease QTLFlowering time
QTL
Ht2
Htn1
Fig. 1. Chromosomal regions associated with multiple disease resistance
qEt8.06 is the largest-effect NLB-QTL identified in the nested association mapping (NAM) populationnested association mapping (NAM) population
The nested association mapping (NAM) population is a large-scale mapping resource in maize, consisting of 5,000 recombinant inbred lines (RILs) developed from 25 diverse inbred lines crossed with a common inbred line B73. This resource is designed to combine the advantages of linkage mapping and association mapping, for high resolution QTL mapping with genome-wide coverage (7). Evaluating a subset of the NAM population for NLB for a first year led to mapping of 6 QTLs conditioning increased incubation period (IP) and 15 QTLs conditioning decreased disease severity (AUDPC) (Fig. 2). Of the 21 QTL detected, qEt8.06 (qEt for quantitative resistance to Exserohilum turcicum) was identified as the largest-effect QTL across all populations, and one of the two QTLs significantly contributing to both resistance parameters, IP and AUDPC (relative allele effects for decreasing AUDPC shown in Fig. 3). Most of the QTLs identified in this study co-localized with previously reported disease resistance QTLs for NLB, but novel QTLs were also detected.
Fig. 2. Position and relative effect of QTL for resistance to Northern Leaf Blight referenced against previously reported QTL.
IPAUDPC
0
5
10
15
20
DK888 S11
DK888 S11
EtNY001 race 0 race 1 race 23N
DK888 S11
DK888 S11
10
20
15
5
0
Incu
batio
n pe
riod
Resistance spectrum of qEt8.06Although DK888 harbors multiple disease resistance, the DK888 allele at 8.06 (qEt8.06DK888 ) is effective only for NLB resistance. Resistance spectra and effectiveness of diverse alleles at this locus will be characterized in NIL pairs being developed from the NAM population.
Race specificity of qEt8.06qEt8.06DK888 conditions resistance to race 0, race 1, but not race23N of E. turcicum. Race specificity suggests that it may encompass the major genes Ht2 and/orHtn1.
Gene action at qEt8.06qEt8.06 identified in DK888 HIF showed partially dominant resistance, differing from the completely dominance of Ht2 documented in previous reports (6).
11
12
13
14
15
16
17
18
DK888 Het S11
Allele(s) at umc2210
Incu
batio
n pe
riod
(day
s af
ter i
noc.
)
Genotype - Genotype IP difference P-valueDK888/DK888 S11/S11 3.8 days < 0.0001 ***
DK888/DK888 Heterozygote 3.2 days < 0.0001 ***
Heterozygote S11/S11 0.6 days 0.0119 *
References1. Carson and van Dyke (1994) Plant Dis. 78: 519-522.2. Tuinstra et al. (1997) Theor. Appl. Genet. 95: 1005-
1011.3. Simcox and Bennetzen (1993) Phytopathology 83: 1326-1330.4. Wisser et al. (2006) Phytopathology 96: 120-129.
5. Wisser et al. (2008) Genetics (in press).6. Yin et al. (2003) Chinese Science Bulletin 48(2): 165-
169.7. Yu et al. (2008) Genetics 178: 539-551.
Genetic dissection of qEt8.06The QTL interval for qEt8.06DK888 in F7 was ~20 Mb. Trait-marker association with ~2,800 individuals (F9 or F10) segregating for bin 8.06 has delimited the resistance locus to a region of < 4 Mb tightly linked to the marker umc2210. High marker density in the NAM population also allowed mapping of qEt8.06 to an overlapping region. Since all available SSR markers have been exhausted in the region, we have started to develop single nucleotide polymorphism markers (SNPs) surrounding umc2210. We are working to further saturate the resistance locus with SNPs to identify further recombinants for positional cloning.
Previously reported NLB-QTL
Chr. 1 Chr. 2 Chr. 3 Chr. 4 Chr. 5 Chr. 6 Chr. 7 Chr. 8 Chr. 9 Chr. 10
-0.9
-0.8
-0.7
-0.6
-0.5
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
Ki1
1
CM
L52
CM
L247
CM
L333
NC
358
MS7
1
Oh4
3
CM
L228
CM
L322
B97 P3
9
M37
W
M16
2W
CM
L69
Tx30
3
CM
L277
Ky2
1
Mo1
8W Tzi8
NC
350
Il14H B73
CM
L103 Ki3
Hp3
01
Oh7
B
Maize genotype
Rel
ativ
e al
lele
effe
ct(L
Smea
n of
AU
DPC
sta
ndar
dize
d to
B73
)
Fig. 3. Relative allele effects for qEt8.06
from 25 NAM parents
Negative values:lower disease severity relative to the common parental line B73.
qEt8.06 explains the most genetic variance of NLB resistance in NAM.
0
10
20
30
40
50
60
70
80
90
- Log
P
GH (Dec 07; n = 576)GH (May 08; n = 1191)Aurora NY (Jul 08; n = 1043)
QTL region identified in F7
umc1
8 28
umc1
9 97
umc2
3 95
umc2
3 56um
c11 49
bnlg
24 0
umc2
3 61
umc2
1 99
umc1
7 77um
c13 16
bnlg
17 24
umc1
7 28
umc1
2 87
umc2
2 10
Evidence for NLB-QTLs in maize bin 8.05-8.06
umc1
828
umc1
997
umc2
395
umc2
356
umc1
149
bnlg
240
umc2
361
umc2
199
umc1
777
umc1
316
bnlg
1724
umc1
728
umc1
287
umc2
210
130 135 140 145 150 155
8.05 8.06
115 120 125um
c237
8
umc1
712
umc1
846
110
umc2
367
bnl2
.369
qEt8.06 in NAM
qEt8.06DK888
Ht2 (6) Htn1 (3)NLB-QTL
qEt8.06 in recurrent selection population (5)
** * * ** * **
* Putatively selected loci in recurrent selection population (5).
Htn1• Susceptible lesion type• Delay of lesion
development• Partially dominant,
genetic background dependent
Ht2• Chlorotic lesion type• Fewer lesions, prolonged
incubation period• Dominant, resistance breaks
down at low light intensities
umc1
121
Ht2 (3)
Physical map of bin 8.05-8.06 in maize
BackgroundNorthern Leaf Blight (NLB), caused by Exserohilum turcicum, is one of the most important diseases affecting maize production worldwide. Several qualitative loci (Ht genes) and a large number of quantitative trait loci (QTL) for NLB resistance have been identified and widely used in breeding programs for disease control. Qualitative race-specific resistance of Ht genes is characterized as inducing hypersensitive response and/or delaying lesion development, in a monogenic manner. However, the expression of Ht genes can be quantitative in certain environments and genetic backgrounds (1). Co-localization of major R genes and disease QTLs in some chromosomal regions of the maize genome (4) also suggests that the distinction between qualitative and quantitative resistance is ambiguous. Isolating and characterizing gene(s) underlying resistance loci is needed for resolving the question.