Genetic dissection and validation of a new dominant QTL associated with chlorophyll content and its regulatory networks analysis in soybean

Leaf-color mutants have proven valuable for studying chlorophyll metabolism, photosynthesis, and yield improvement. In this study, we identified a yellow-leaf (yl) mutant in soybean (Glycine max), characterized by reduced chlorophyll accumulation, lower net photosynthesis rate, and fewer grain number per plant than the wild type. To identify genes associated with chlorophyll content, we performed a large-scale linkage mapping study using recombinant inbred lines from a cross between the yl mutant and a green-leaf cultivar across three environments. Using quantitative trait locus sequencing (QTL-seq) analysis, we mapped 12 QTL to chromosomes 5, 13, 15, 19, and 20. Of these QTL, one new dominant locus with the largest LOD, named qCC1, was identified consistently and explained 31.73% of the total phenotypic variation on average. Notably, qCC1 was also associated with yield-related traits, including plant height and pod number per plant. Fine-mapping narrowed down qCC1 to an 82.29-kb region. Within this interval, we identified Glyma.15 g087500.1, encoding an ankyrin repeat-containing protein, as the most likely candidate gene, because its homologs are reported to function in thylakoid membrane biogenesis during plastid development. Phenotypic analysis of near-isogenic lines (NILs) revealed that those harboring the qCC1 allele conferring green leaves displayed significantly enhanced chlorophyll content by 136.53%–323.92%, net photosynthesis rate by 11.64%–42.13%, and yield by 111.32% compared with NILs carrying the allele conferring yellow leaves. Comparative transcriptome profiling of NILs coupled with RT-qPCR validation demonstrated that qCC1 up-regulated one differentially expressed gene (DEG) associated with chlorophyll biosynthesis and six DEGs related to photosystem, whereas it down-regulated one gene involved in chlorophyll degradation. These findings provide valuable insights into the biological function and regulatory mechanism of chlorophyll metabolism and offer guidance for breeding soybean varieties with enhanced photosynthetic efficiency and high yield.