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Nat Genet. 2019 Jun;51(6):1052-1059. doi: 10.1038/s41588-019-0427-6. Epub 2019 May 31.

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement.

Author information

1
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
2
BGI Genomics, BGI Shenzhen, Shenzhen, China.
3
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
4
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. yjianbing@mail.hzau.edu.cn.

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.

PMID:
31152161
DOI:
10.1038/s41588-019-0427-6
[Indexed for MEDLINE]

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