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

Leaf morphology traits determine photosynthetic efficiency, high-density planting tolerance, and grain yield in maize (Zea mays L.). Understanding the genetic basis of these traits is of great practical significance for optimizing plant architecture and enhancing photosynthetic capacity to improve grain yield. 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 representative 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 morphology traits—leaf length (LL), leaf width (LW), and leaf angle (LA)—in these populations were evaluated over two years and across two field locations in China. The inclusive composite interval mapping (ICIM) approach was used to identify quantitative trait loci (QTLs) and candidate genes associated with heterosis for leaf morphological traits. The results showed that more QTLs for 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 LW and 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—the ones expressed in maize leaves—were identified, among which Zm00001d022618 and Zm00001d008625 play crucial roles in regulating heterosis formation of leaf morphological traits. 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.