QTL mapping and epistasis analysis of brace root traits in maize

Root architecture is a major factor influencing root lodging, which limits greater yield stability at high planting density. Total brace root tier number (TBRTN) and effective brace root tier number (EBRTN) are the two most important root architecture traits influencing root lodging. However, the genetic mechanisms that underlie these traits remain poorly understood. In this study, quantitative trait loci (QTL) for TBRTN and EBRTN were mapped using a set of 201 recombinant inbred lines (RILs) and 278 immortalized F2 (IF2) populations derived from these RILs, which were evaluated in three environments. Ten QTL in the RILs and 15 QTL in the IF2 population were detected. In the two populations, we identified two coincident major QTL for TBRTN and a single identical major QTL for EBRTN. The QTL for TBRTN showed the largest additive effect, accounting for 16.36 and 17.88% of the phenotypic variance in the RILs and IF2 population, respectively. Additional epistatic effects were identified for all the maize chromosomes, except for chromosome 4. Most epistatic effects involved pairs of loci that were on different chromosomes. At the same time, we found loci that interacted simultaneously with several other loci to affect expression of the traits, which was particularly evident in the IF2 population. For example, qTAR1-2 interacted simultaneously with qTAR2-1, qTAR3-1, qTAR5-1, and qITAR8-2 to affect the expression of TBRTN. Therefore, a complex network controlling the traits was found in maize. These results provide useful information for understanding the molecular mechanisms controlling root architecture.