Genetic diversity provides the foundation for plant breeding and genetic research. Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome (3KRG) Project. We added four additional Indian rice accessions to create a panel of 3004 accessions. However, such a large collection of germplasm is difficult to preserve and evaluate. The construction of core and mini-core collections is an efficient method for the management of genetic resources. In this study, we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from the original panel. The mini-core was validated using different statistical analyses and contained representatives from all major rice groups, including japonica, indica, aus/boro, and aromatic/basmati. Genome-wide association analyses of the mini-core panel efficiently reproduced the marker–trait associations identified in the original panel. Haplotype analysis validated the utility of the mini-core panel. In the current era with many ongoing large-scale sequencing projects, such a strategy for mini-core design should be useful in many crops. The rice mini-core collection developed in this study would be valuable for agronomic trait evaluation and useful for rice improvement via marker-assisted molecular breeding.

遗传多样性为植物育种和遗传研究提供了基础。作为 3K 水稻基因组 (3KRG) 项目的一部分，最近对 3000 多个水稻基因组进行了测序。我们添加了另外 4 个印度稻米品种，创建了一个包含 3004 个品种的面板。然而，如此大量的种质资源很难保存和评估。核心和微型核心种质的建设是遗传资源管理的有效方法。在这项研究中，我们开发了一个包含 520 个种质的迷你核心，它捕获了大部分 SNP，并代表了原始组中的所有表型和地理区域。迷你核心使用不同的统计分析进行验证，包含来自所有主要稻米类别的代表，包括粳稻、籼稻、aus / boro和香稻/印度香米。迷你核心面板的全基因组关联分析有效地再现了原始面板中识别的标记-性状关联。单倍型分析验证了迷你核心面板的实用性。在当今时代，有许多正在进行的大规模测序项目，这种微型核心设计策略应该对许多作物有用。本研究开发的水稻迷你核心种质对于农艺性状评估具有重要价值，并且有助于通过标记辅助分子育种进行水稻改良。