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Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

Abstract

Maize kernel oil is a valuable source of nutrition. Here we extensively examine the genetic architecture of maize oil biosynthesis in a genome-wide association study using 1.03 million SNPs characterized in 368 maize inbred lines, including 'high-oil' lines. We identified 74 loci significantly associated with kernel oil concentration and fatty acid composition (P < 1.8 × 10−6), which we subsequently examined using expression quantitative trait loci (QTL) mapping, linkage mapping and coexpression analysis. More than half of the identified loci localized in mapped QTL intervals, and one-third of the candidate genes were annotated as enzymes in the oil metabolic pathway. The 26 loci associated with oil concentration could explain up to 83% of the phenotypic variation using a simple additive model. Our results provide insights into the genetic basis of oil biosynthesis in maize kernels and may facilitate marker-based breeding for oil quantity and quality.

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Figure 1: Manhattan and quantile-quantile plots resulting from the GWAS results for oil concentration in maize kernels.
Figure 2
Figure 3: Associations and genomic locations of known and new loci associated with oil concentration and composition.

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Acknowledgements

We appreciated the helpful comments on the manuscript from A. Rafalski, J. Dudley, T. Setter and B. Shen. This research was supported by the National Hi-Tech Research and Development Program of China (2012AA10A307), the National Natural Science Foundation of China (31101156, 31123009), the National Basic Research Program of China (2009CB118404), the Ministry of Agriculture of China (2011ZX08009-001) and the National Gene Bank Project of China.

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J.Y., X.Y., J. Li and G.W. designed and supervised this study. H.L., W.W., Y.H., Y. Chai, P.Z. and X.H. performed the experiments. H.L., X.Y., W.W., Z.P., J.F., T.G., N.Y., Y.L., J. Liu, Y. Cheng and J.Y. analyzed data. J.W. and J.Z. contributed new regents. J.Y., H.L. and M.L.W. prepared the manuscript, and all the authors critically read and approved the manuscript.

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Correspondence to Guoying Wang, Jiansheng Li or Jianbing Yan.

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Li, H., Peng, Z., Yang, X. et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45, 43–50 (2013). https://doi.org/10.1038/ng.2484

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