QTL Mapping of SPAD Values Associated with Leaf Color in Bunching Onion

Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with leaf color using SPAD values as a phenotypic indicator. Methods: An F2 population derived from a cross between the dark green line YSG1go and the light green line Asagikei-KUJYO was used. A linkage map was constructed based on RNA-seq-derived SNP markers, and SPAD values were measured for QTL analysis. Results: The linkage map consisted of eight linkage groups with a total length of 2103.0 cM and 765 mapped markers. SPAD values showed significant differences between the parental lines, with high broad-sense heritability (H2 = 0.76), indicating a strong genetic contribution to this trait. Multiple significant QTLs were detected on chromosomes 4 and 5, each explaining 27.4–38.1% of the phenotypic variance. The direction of allelic effects differed among QTLs, suggesting that favorable alleles are distributed between the parental lines. In addition, genes related to chloroplast protein translation were identified within the QTL regions. Conclusions: SPAD values are a suitable indicator for genetic analysis of leaf color in bunching onion, and the QTLs identified in this study provide valuable information for molecular breeding aimed at improving dark green leaf color.