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.

玉米是全球最重要的农作物之一，它显示出显着的遗传多样性。了解这种多样性可以帮助改善作物；然而，仅对现代温带品种阐明了金标准基因组。在这里，我们介绍了一个玉米小内核近交系的高质量参考基因组（15.78 megabase的重叠群N50），它来自热带地方品种。使用衍生自B73，Mo17和SK的单倍型图谱，我们鉴定了521个不同系中的80,614个多态性结构变异。传统的基于单核苷酸多态性的方法无法检测到其中约22％的变异，其中一些变异会影响基因表达和性状表现。为了说明各种SK系列的实用性，我们使用它对控制籽粒重量的主要效应定量性状基因座（基于玉米改良过程中选择的关键性状）进行基于图谱的克隆。潜在的候选基因ZmBARELY ANY MERISTEM1d为提高农作物产量提供了目标。