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Genetic Dissection of Loci Conditioning Disease Resistance in Maize Bin 8.06 Chia-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 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 Background qEt8.06 is the largest-effect NLB-QTL identified in the nested association mapping (NAM) population Fig. 1. Chromosomal regions associated with multiple disease resistance Viral diseases Erwinia wilt Aspergillus flavus Ear rot and stalk rot Common smut Downy mildew Common rust Southern rust Ht2 Htn1 Northern leaf blight Disease QTL Flowering time QTL 6 Anthracnose stalk rot (ASR) Rust Smut Stewart's wilt Unit Incubation period days after inoculation 17.4 ± 1.7 10.0 ± 0.3 < 0.0001 *** Primary diseased leaf area % 9.0 ± 4.1 65.0 ± 6.2 < 0.0001 *** Lesion length mm 1.2 ± 0.05 1.2 ± 0.06 0.719 Primary diseased leaf area % 29.5 ± 1.0 30.0 ± 1.5 0.585 Incubation period days after inoculation 7.7 ± 0.2 7.8 ± 0.4 0.698 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 Discolored internode tissue Total % of internode to 8 121.7 ± 12.9 120.0 ± 23.0 0.901 1 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 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 Primary diseased leaf area % 72.5 72.5 -0.6 -0.7 -0.8 Oh7B Hp301 Ki3 CML103 B73 Il14H NC350 Tzi8 Mo18W Ky21 CML277 Tx303 -0.9 Maize genotype 0 Chr. 1 Chr. 2 Chr. 3 Chr. 4 Chr. 5 Chr. 6 Chr. 7 Previously reported NLB-QTL Chr. 8 Chr. 9 Chr. 10 Bins EtNY001 Race specificity of qEt8.06 Conclusions race 0 race 1 1. Consistent detection of qEt8.06 in diverse mapping populations indicates that it accounts for a large proportion of NLB resistance in maize germplasm. race 23N 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. qEt8.06DK888 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. – qEt8.06 explains the 2 20 20 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. 15 15 10 10 5 5 0 0 DK888 S11 DK888 S11 DK888 S11 DK888 S11 Gene action at qEt8.06 qEt8.06 identified in DK888 HIF showed partially dominant resistance, differing from the completely dominance of Ht2 documented in previous reports (6). Genotype - Genotype DK888/DK888 S11/S11 IP difference 3.8 days P-value 18 16 13 11 3.2 days < 0.0001 *** Heterozygote S11/S11 0.6 days 0.0119 * • Chlorotic lesion type • Fewer lesions, prolonged incubation period • Dominant, resistance breaks down at low light intensities 14 < 0.0001 *** Heterozygote Ht2 15 12 DK888/DK888 Evidence for NLB-QTLs in maize bin 8.05-8.06 17 DK888 Het Htn1 qEt8.06 in NAM qEt8.06 in recurrent selection population (5) NLB-QTL Ht2 (3) Ht2 (6) Allele(s) at umc2210 Htn1 (3) - Log P individuals (F9 or F10) segregating for bin 8.06 has delimited the resistance locus to a region of < 4 70 Aurora NY (Jul 08; n = 1043) Physical map of bin 8.05-8.06 in maize umc2210 145 140 umc2199 umc1121 umc1777 umc1316 umc1712 umc2378 135 150 155 * Putatively selected loci in recurrent selection population (5). 50 40 30 20 Mb tightly linked to the marker umc2210. High marker density in the NAM population also allowed 10 bnlg1724 umc2395 umc1997 umc1728 umc2361 umc2356 umc1149 bnlg240 umc1828 umc1287 umc2210 umc1777 umc1316 QTL region identified in F7 umc2199 0 mapping of qEt8.06 to an overlapping region. Since all available SSR markers have been exhausted surrounding umc2210. We are working to further saturate the resistance locus with SNPs to identify GH (May 08; n = 1191) 130 60 The QTL interval for qEt8.06DK888 in F7 was ~20 Mb. Trait-marker association with ~2,800 in the region, we have started to develop single nucleotide polymorphism markers (SNPs) 80 125 8.06 * umc1287 umc1828 Genetic dissection of qEt8.06 GH (Dec 07; n = 576) 120 ** umc1846 90 umc2367 bnl2.369 115 • Susceptible lesion type • Delay of lesion development • Partially dominant, genetic background dependent qEt8.06DK888 S11 110 further recombinants for positional cloning. References Carson and van Dyke (1994) Plant Dis. 78: 519-522. Tuinstra et al. (1997) Theor. Appl. Genet. 95: 1005-1011. Simcox and Bennetzen (1993) Phytopathology 83: 1326-1330. Wisser et al. (2006) Phytopathology 96: 120-129. CML69 -0.5 8.05 1. 2. 3. 4. M162W M37W P39 B97 CML322 CML228 Oh43 MS71 NC358 CML333 CML247 CML52 Ki11 Negative values: lower disease severity relative to the common parental line B73. -0.4 4 Incubation period (days after inoc.) Northern leaf blight (NLB) Southern leaf blight (SLB) Anthracnose leaf blight (ALB) Parameter -0.3 AUDPC Incubation period Disease -0.2 most genetic variance of NLB resistance in NAM. To 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. Student's t-test (P-value) -0.1 IP Characterization of qEt8.06 using near-isogenic line (NIL) pairs Allele(s) at qEt8.06 DK888 S11 0 Fig. 2. Position and relative effect of QTL for resistance to Northern Leaf Blight referenced against previously reported QTL. -2 Resistance spectrum of qEt8.06 Although 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. 0.1 umc1997 * umc1728 umc2361 ** umc2395 bnlg1724 Chromosome 8 Southern leaf blight 0.2 * umc2356 ** umc1149 bnlg240 Maize disease QTL consensus map (Wisser et al., 2006) Gray leaf spot Fig. 3. Relative allele effects for qEt8.06 from 25 NAM parents 8 QTL effect (R2 across all populations) 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. 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. (LSmean of AUDPC standardized to B73) Northern 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. Relative allele effect 1 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. 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 University Margaret Smith Dept. of Plant Breeding and Genetics, Cornell University Funding from Ministry of Education, Taiwan; the Generation Challenge Program; and The McKnight Foundation.