Genome-wide dissection of changes in maize root system architecture during modern breeding

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. The root-related changes in maize domestication, improvement and modern breeding were systematically investigated, and candidate genes related to maize root system architecture were identified for future genetic improvement.

Automated summary

In this study, we identified candidate genes associated with maize root system architecture (RSA) through an association mapping panel. We also found that modern breeding has favored a steeply angled root system. Additionally, we confirmed the role of two auxin-related genes in regulating root angle and depth in maize.