QTL mapping, validation, and candidate gene predicting for maize plant architecture traits via bulked segregant analysis plus linkage analysis with F₂ population

Maize (Zea mays L.) is a globally important food crop whose plant architecture directly influences yield formation by regulating lodging resistance and photosynthetic efficiency, so deciphering the genetic mechanisms underlying plant architecture traits is essential for breeding high-yield varieties. In this study, maize inbred lines C144 and Su54—exhibiting significant differences in plant height (PH), tassel branch number (TBN), and leaf angle (LA)—were selected as parents; we first conducted preliminary QTL (Quantitative Trait Locus) mapping using BSA (bulked segregant analysis) to construct extreme phenotype bulks, then combined phenotypic data from the F₂ segregating population to build a genetic map with QTL IciMapping V4.2 software, and validated QTL loci via ICIM (inclusive composite interval mapping). The results revealed five validated major plant architecture-related QTLs: two for PH, qPH5-1 on chromosome5 (phenotypic variation explained [PVE] = 13.75%, LOD (Logarithm of Odds) = 19.87) and qPH9-1 on chromosome9 (PVE = 6.69%, LOD = 9.73); one for TBN, qTBN5-1 on chromosome5 (PVE = 6.37%, LOD = 7.6); and two for LA, qLA5-1 (penultimate leaf angle) on chromosome5 (PVE = 6.16%, LOD = 7.2) and qLA5-2 (above-ear leaf angle) on chromosome5 (PVE = 9.74%, LOD = 11.69). Based on gene annotation and functional prediction within these QTL intervals, six candidate genes were identified: Zm00001eb238970 and Zm00001eb238980 (encoding P21-Arc proteins, subunits of the ARP2/3 complex) in qPH5-1; Zm00001eb394120 (encoding a protein phosphatase 2 C) in qPH9-1; Zm00001eb243000 (encoding an E2F transcription factor) in qTBN5-1; Zm00001eb243750 (encoding a GTP/ATP-binding protein) in qLA5-1; and Zm00001eb233650 (encoding a SUN family protein with Sad1/UNC domains) in qLA5-2. These novel QTL loci and candidate genes provide critical insights into the genetic regulatory network of maize plant architecture and can directly support molecular marker-assisted breeding to accelerate the development of high-yield and dense-tolerant maize varieties.