Yang, N., Liu, J., Gao, Q., Gui, S., Chen, L., Yang, L., Huang, J., Deng, T., Luo, J., He, L., Wang, Y., Xu, P., Peng, Y., Shi, Z., Lan, L., Ma, Z., Yang, X., Zhang, Q., Bai, M., Li, S., Li, W., Liu, L., Jackson, D., Yan, J. (June 2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet, 51 (6). pp. 1052-1059. ISSN 1061-4036
Abstract
Maize is one of the most important crops globally, and it shows remarkable genetic diversity. Knowledge of this diversity could help in crop improvement; however, gold-standard genomes have been elucidated only for modern temperate varieties. Here, we present a high-quality reference genome (contig N50 of 15.78 megabases) of the maize small-kernel inbred line, which is derived from a tropical landrace. Using haplotype maps derived from B73, Mo17 and SK, we identified 80,614 polymorphic structural variants across 521 diverse lines. Approximately 22% of these variants could not be detected by traditional single-nucleotide-polymorphism-based approaches, and some of them could affect gene expression and trait performance. To illustrate the utility of the diverse SK line, we used it to perform map-based cloning of a major effect quantitative trait locus controlling kernel weight-a key trait selected during maize improvement. The underlying candidate gene ZmBARELY ANY MERISTEM1d provides a target for increasing crop yields.
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