QTL analysis for plant architecture-related traits in maize under two different plant density conditions

The erectophile plant architecture in maize is responsible for high plant density tolerance, yet the genetic basis for this relationship remains elusive, especially for how canopy architecture and plant height related traits at different positions respond to plant density. In this study, nine canopy traits and six plant height (PH) traits were evaluated across four environments under low plant density (57,000 plants/ha, LD) and high plant density (114,000 plants/ha, HD), using a set of 301 recombinant inbred lines originating from two foundation parents in China, the inbred lines YE478 and 08-641. In total, 176 quantitative trait loci (QTLs) for plant architecture related traits (94 only in LD, 44 only in HD and 38 under both densities) and 36 QTL clusters were detected via combined analysis. We identified 21 sharing QTL regions associated with plant height, leaf width and leaf angle at different positions. These results suggest that plant architecture-related traits were greatly influenced by density-specific and environment-specific alleles, and epistasis, QTL × environment interaction and QTL pleiotropy also play essential roles for plant architecture via complex interactions. Though PH-related traits, leaf widths and leaf angles at different positions could be partially affected by several common QTLs, there are still different genetic mechanisms of plant architecture response to plant density. Furthermore, elite line YE478 provided most of the favorable plant architecture alleles for high-density tolerance. Five QTL clusters containing six major QTLs, were useful for further studies of plant architecture and will provide helpful information for ideal plant type, high-density tolerance and marker-assisted selection.