Genome differentiation has shaped the divergence in element concentration between rice subspecies and contributed to the correlation among trace minerals in the rice grain. The balance between trace minerals in rice, a staple food for more than half of the world's population, is crucial for human health. However, the genetic basis underlying the correlation between trace minerals has not been fully elucidated. To address this issue, we first quantified the concentrations of 11 trace minerals in the grains of a diversity panel of 575 rice cultivars. We found that eight elements were accumulated at significantly different levels between the indica and japonica subspecies, and we also observed significant correlation patterns among a number of elements. Further, using a genome-wide association study, we identified a total of 96 significant association loci (SALs). The differentiation of the major-effect SALs along with the different number of high-concentration alleles present in the two subspecies shaped the different element performance in indica and japonica varieties. Only a few SALs located in clusters and the majority of SALs showed subspecies/subgroup differentiation, indicating that the correlations between elements in the diversity panel were mainly caused by genome differentiation instead of shared genetic basis. The genetic architecture unveiled in this study will facilitate improvement in breeding for trace mineral content.

中文翻译：

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水稻籽粒微量矿物质积累和元素相关性的亚种遗传结构差异。

基因组分化形成了水稻亚种之间元素浓度的差异，并促成了水稻籽粒中微量矿物质之间的相关性。大米是世界一半以上人口的主食，大米中的微量矿物质之间的平衡对人类健康至关重要。然而，微量矿物质之间相关性的遗传基础尚未完全阐明。为了解决这个问题，我们首先量化了 575 个水稻品种的多样性面板中 11 种微量矿物质的浓度。我们发现籼稻和粳稻亚种之间有八种元素以显着不同的水平积累，并且我们还观察到一些元素之间存在显着的相关模式。此外，使用全基因组关联研究，我们确定了总共 96 个重要的关联位点 (SAL)。主要效应 SAL 的差异以及两个亚种中存在的不同数量的高浓度等位基因塑造了籼稻和粳稻品种中不同的元素表现。只有少数 SAL 位于簇中，大多数 SAL 表现出亚种/亚群分化，表明多样性面板中元素之间的相关性主要是由基因组分化而不是共享遗传基础引起的。本研究中揭示的遗传结构将有助于改善微量矿物质含量的育种。主要效应 SAL 的差异以及两个亚种中存在的不同数量的高浓度等位基因塑造了籼稻和粳稻品种中不同的元素表现。只有少数 SAL 位于簇中，大多数 SAL 表现出亚种/亚群分化，表明多样性面板中元素之间的相关性主要是由基因组分化而不是共享遗传基础引起的。本研究中揭示的遗传结构将有助于改善微量矿物质含量的育种。主要效应 SAL 的差异以及两个亚种中存在的不同数量的高浓度等位基因塑造了籼稻和粳稻品种中不同的元素表现。只有少数 SAL 位于簇中，大多数 SAL 表现出亚种/亚群分化，表明多样性面板中元素之间的相关性主要是由基因组分化而不是共享遗传基础引起的。本研究中揭示的遗传结构将有助于改善微量矿物质含量的育种。