Mapping QTL for Plant Architecture-Related Traits in Soybean Across Multiple Environments

Improving soybean plant architecture is critical for enhancing yield potential. To dissect the genetics of related traits, a recombinant inbred line population of 175 F9:12 families (derived from Glycine max cultivars Jidou 12 [female] × Ji NF58 [male]) was used for quantitative trait locus (QTL) mapping. Four key traits—plant height, bottom pod height, node number on main stem, and branch number—were analyzed across six environments (two growing seasons × three locations) via two methods: composite interval mapping (CIM, QTL Cartographer v2.5) and mixed-model-based composite interval mapping (MCIM, QTLNetwork 2.0). A total of 22 stable QTLs were detected, with phenotypic variation explained (PVE) of 1.2–52.5%. Co-localized QTLs (due to significant trait correlations) concentrated in three genomic intervals: Satt286-Sat_251 (LG C2/chromosome 06), Satt156-Satt229 (LG L/chromosome 19), and Satt581-Sat_190 (LG O/chromosome 10). A novel QTL (qBPH-O-2) for bottom pod height was identified on LG O. Major QTLs with QTL-by-environment (QE) interactions were found on LG A1 (plant height, node number on main stem) and qBN-C2-1 (branch number, high additive effects + QE interactions). These findings support marker-assisted selection (MAS), targeted plant architecture improvement, and gene pyramiding in soybean breeding.