Integrated QTL mapping and functional analysis reveal GmDWF4.2 as a key regulator of soybean plant height

Plant height is a key agronomic trait in soybean that is closely associated with yield potential. Nevertheless, the molecular mechanisms underlying its regulation remain largely elusive. In this study, we employed a recombinant inbred line (RIL) population comprising 271 lines evaluated across six environments to dissect the genetic architecture of plant height. A total of eleven quantitative trait loci (QTLs) associated with plant height were identified, including four novel loci (qPH5-1, qPH6-1, qPH6-2, and qPH17-1). Among these, four stable major QTLs (qPH2-1, qPH10-1, qPH18-1, and qPH19-2) were consistently detected across multiple environments, each explaining more than 10 % of the phenotypic variance. Resequencing analysis of the parental lines suggested that E1, E2, Dt2, and E3 represent candidate genes underlying qPH6-3, qPH10-1, qPH18-1, and qPH19-2, respectively. Importantly, Glyma.02G057500 (GmDWF4.2), a soybean ortholog of Arabidopsis AtDWF4, was mapped within the qPH2-1 interval and exhibited exon polymorphisms between the two parental lines, Jidou17 and Suinong14. Functional assays demonstrated that both GmDWF4.2_JD17 and GmDWF4.2_SN14 partially rescued the dwarf phenotype of the Arabidopsis dwf4-102 mutant. Notably, heterologous overexpression of GmDWF4.2_SN14 in wild-type Arabidopsis resulted in a significantly greater increase in plant height compared to that of GmDWF4.2_JD17. Overall, our findings demonstrate that GmDWF4.2 functions as a positive regulator of plant height in soybean and further reveal that the GmDWF4.2_SN14 haplotype confers a stronger promotive effect on this trait. These findings contribute to elucidating the genetic regulatory mechanisms of soybean plant height and provide a theoretical foundation for refining molecular marker-assisted selection strategies for this agronomic trait.