Genetic dissection of crown root traits and their relationships with aboveground agronomic traits in maize

The crown root system is the most important root component at both the vegetative and reproductive stages in maize. However, the genetic basis of maize crown root traits (CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits is poorly understood in maize. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits including flowering time, plant architecture and grain yield. Using a genome-wide association study (GWAS) coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one third of the genetic variation in crown root was co-located with 46 QTL derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication- and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection during domestication and improvement in maize. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during domestication and improvement in maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics enabled improvements in maize root architecture.