Quantitative trait loci mapping of heterosis for leaf morphological traits and candidate gene identification in maize

Background Leaf morphology determines photosynthetic efficiency, high-density planting tolerance, and grain yield in maize. Understanding the genetic basis of these traits is of great practical significance for optimizing plant architecture and enhancing photosynthetic capacity to improve yield. Results In this study, six maternal and paternal testcrossing (TC/M and TC/P) populations were developed from recombinant inbred line (RIL) populations using three inbred lines—Y46 (tropical), Ye107 (temperate), and MON2 (subtropical)—in pairwise crosses. The inbreds represented the most characteristic lines from the three major heterotic groups: Suwan, Reid, and Non-Reid. Each RIL population was backcrossed to maternal and paternal parents, to generate TC/M and TC/P populations, respectively. All individuals from these testcross populations (TCM/Ps) were genotyped using genotyping-by-sequencing technology. Phenotyping for mid-parent heterosis of leaf architecture traits in these populations was conducted across 2 years and two location field evaluations. Genome-wide association analysis was conducted to identify quantitative trait loci (QTLs) and candidate genes associated with heterosis for leaf morphological traits. The results showed that more QTLs for leaf length (LL) were identified in the Suwan × Non-Reid and Reid × Non-Reid heterotic groups than in Suwan × Reid heterotic groups. However, the largest QTL effects—with a phenotypic variance explained (PVE) of 23.31% for LL—were observed in the Reid × Non-Reid heterotic group. For leaf width (LW) and leaf angle (LA), more QTLs were detected in the Reid × Non-Reid and Suwan × Reid heterotic groups than in the Suwan x Non-Reid heterotic groups. The largest QTL effects were observed in the Reid × Non-Reid heterotic group, with a PVE of 32.32% for LW and 23.13% for LA. In total, seven stable QTLs and 14 candidate genes were identified. Through gene expression analysis, six candidate pleiotropic genes were identified, among which Zm00001d022618 and Zm00001d008625 play crucial roles in regulating heterosis formation of leaf morphological traits. Conclusion These findings provide insights into the complexity of heterosis determination in leaf morphological traits and may support precision breeding to optimize plant architecture and harness heterosis in maize.