Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement.
Nat Genet, 2019/06;51(6):1052-1059.
Yang N[1], Liu J[1], Gao Q[2], Gui S[1], Chen L[1], Yang L[2], Huang J[1], Deng T[2], Luo J[1], He L[2], Wang Y[1], Xu P[2], Peng Y[1], Shi Z[2], Lan L[1], Ma Z[2], Yang X[2], Zhang Q[2], Bai M[2], Li S[2], Li W[1], Liu L[1, 3], Jackson D[1, 3], Yan J[4]
Affiliations
PMID: 31152161DOI: 10.1038/s41588-019-0427-6
Impact factor: 41.307
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.
MeSH terms
Computational Biology; Genetic Association Studies; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; Inbreeding; Molecular Sequence Annotation; Phenotype; Plant Breeding; Plants, Genetically Modified; Polymorphism, Single Nucleotide; Quantitative Trait, Heritable; Zea mays
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