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Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

Abstract

Nested association mapping (NAM) offers power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5,000 recombinant inbred lines (RILs) from 25 families representing the global diversity of maize, was evaluated for resistance to southern leaf blight (SLB) disease. Joint-linkage analysis identified 32 quantitative trait loci (QTLs) with predominantly small, additive effects on SLB resistance. Genome-wide association tests of maize HapMap SNPs were conducted by imputing founder SNP genotypes onto the NAM RILs. SNPs both within and outside of QTL intervals were associated with variation for SLB resistance. Many of these SNPs were within or near sequences homologous to genes previously shown to be involved in plant disease resistance. Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions.

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Figure 1: Parental and RIL family mean values ± s.e.m. of SLB index scores.
Figure 2: Genetic map of NAM population with support intervals of 32 QTLs and positions of 51 HapMap SNPs retained in final model for SLB resistance.
Figure 3: Heat map of additive effect estimates of 25 founder inbred alleles at QTLs for SLB resistance relative to B73 on the nine-point SLB index scale.
Figure 4: Results of GWA subsampling analysis.
Figure 5: Linkage disequilibrium.

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Acknowledgements

We thank M. Eller, D. Rhyne, D. Stephens, G. Van Esbroek, C. Herring and the staffs of the North Carolina Central Crops Research Station and 27 Farms, Homestead, Florida, USA, for assistance in the field. We also thank J. Green and C.-R. Shyu for providing the photographs for Supplementary Figure 1. This research was supported by the US National Science Foundation (DBI-0321467 and IOS-0820619) and funds were provided by USDA-ARS. K.L.K. is supported by Pioneer Hi-Bred International.

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Contributions

E.S.B., M.D.M., S.K. and J.B.H. developed the NAM population. K.L.K., R.J.W., A.R.B., M.A.O.-R., J.C.Z., P.J.B.-K. and J.B.H. conducted the field experiments. E.S.B. and D.W. created HapMap data. P.J.B. and E.S.B. developed GWAS methods and software. K.L.K. and J.B.H. analyzed the data. K.L.K., R.J.W., P.J.B.-K. and J.B.H. wrote the paper.

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Correspondence to James B Holland.

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Supplementary Figures 1–9, Supplementary Tables 1–9 and Supplementary Note (PDF 1624 kb)

Supplementary Table 7

Information on 245 significantly associated SNPs. (XLS 138 kb)

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Kump, K., Bradbury, P., Wisser, R. et al. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43, 163–168 (2011). https://doi.org/10.1038/ng.747

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