Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.

适当的根系结构 (RSA) 可以提高密集种植田间的玉米产量，但对其在玉米中的遗传基础知之甚少。在这里，我们对来自关联作图面板的 14,301 种田间种植植物进行了根表型分析，以研究玉米 RSA 的遗传结构。一项全基因组关联研究确定了 81 个高置信度 RSA 相关候选基因，并揭示了在玉米驯化和改良过程中选择了 28 个（24.3%）已知的根相关基因。我们发现现代玉米育种选择了陡峭的根系。与陡根系角度相关的有利等位基因在现代育种过程中不断积累，我们的数据精确定位了在不同育种时代选择的与根相关的基因。我们确认两个生长素相关基因，ZmRSA3.1和ZmRSA3.2有助于调节玉米的根角和深度。我们对 RSA 相关基因的全基因组鉴定为适合高密度种植的玉米育种提供了新的策略和遗传资源。