Identification of quantitative trait loci qPL6 for petiole length in soybean.

key messageA stable QTL for petiole length, qPL6, was mapped in a RIL population over three consecutive growing seasons, with two candidate genes identified through integrated RNA-seq analysis. Petiole length is a critical determinant of canopy architecture in soybean (Glycine max (L.) Merr.), directly modulating yield potential through its effects on photosynthetic efficiency. Consequently, identifying genes controlling petiole length is essential for developing an ideal plant architecture adapted to high-density planting, ultimately increasing yield per unit area. Here we identified a stable quantitative trait locus (QTL) for petiole length on chromosome 6, designated qPL6, across three consecutive growing seasons, which explained 6.13-19.42% of the phenotypic variance. By comparing the longitudinal anatomical structures of petioles from Qi Huang No34 (QH34) and Ji Dou No17 (JD17), we determined that the difference in petiole length was attributed to variations in parenchyma cell lengths. Through RNA-seq analysis of two near-isogenic lines (NILs), we identified 90 differential expressed genes (DEGs) common to the upper, middle and lower petioles. These DEGs were significantly enriched in GO terms related to hormone signaling pathways and cell wall organization. By integrating analysis of sequence variations with transcriptional profiles, we selected two candidate genes, Glyma.06G258000 and Glyma.06G260800, both implicated in the auxin-responsive pathway. Glyma.06G258000 showed differential expression in the petiole, pulvinus and leaf, and carried a 626-bp InDel located 737 bp upstream of its coding region. Glyma.06G260800 contained two SNPs in its second exon that induced two nonsynonymous mutations. The novel QTL and candidate genes identified in this study offer valuable genetic resources for soybean molecular breeding aimed at optimizing plant architecture and increasing yield.