High-resolution quantitative trait loci mapping and pyramiding effects of candidate genes for plant height in soybean

Plant height is a crucial agronomic trait that significantly influences plant architecture and yield in soybean (Glycine max (L.) Merr.). Identifying major genes regulating plant height and developing closely linked molecular markers are crucial for breeding soybean cultivars with ideal architecture. In this study, a recombinant inbred line (RIL) population (F_2:7-8) developed from a cross between two soybean cultivars with contrasting plant heights was used to conduct quantitative trait loci (QTL) mapping for plant height across five environments based on a high-density genetic linkage map. As a result, 13 QTL associated with plant height were identified on seven chromosomes. Among these, four QTL (qPH-5, qPH6-1, qPH18, and qPH19-2) were consistently detected across multiple environments. Candidate genes for three stable QTL (qPH6-1, qPH18, and qPH19-2) with major effects on plant height were identified by annotating single-nucleotide polymorphisms within the parental haplotypes, combined with analyses of gene expression patterns and biological functions. Consequently, TCP13, Dt2, and Dt1 were predicted as strong candidate genes influencing plant height within these loci, respectively. Haplotype analyses within RIL population and across diverse soybean germplasm revealed that allelic variation in each of these genes significantly affected plant height. Moreover, different haplotype combinations of the three genes exhibited distinct phenotypic effects, indicating a pyramiding effect of these three genes on plant height. These findings will facilitate molecular breeding of soybean cultivars with ideal plant architecture.