The yellow green plant (Clygp) encodes a signal recognition particle 54 kDa protein regulating chloroplast development and photosynthesis in watermelon

Photosynthesis serves as the primary source of nutrients synthesized in higher plants, and enhancing photosynthetic efficiency can significantly improve crop yield and fruit quality. Leaf color mutants, which are ideal materials for studying chloroplast development and photosynthesis mechanisms, have been extensively investigated in field crops. However, the study on their application in watermelon remains limited. In this study, we identified a yellow-green phenotype mutant, PKH352, from an EMS mutagenesis watermelon mutant library. The chlorophyll content and maximal photochemical efficiency in PKH352 was significantly reduced. Genetic analysis showed that the mutated trait was controlled by a single nuclear gene, which named as Clygp (Citrullus lanatus yellow-green plant). Through MutMap and linkage analysis in an F2 population of 440 plants, we identified a single nucleotide polymorphism (SNP) mutation in ClG42_04g0106300, which encoded a signal recognition particle 54 kDa protein, as the causal variant for the yellow-green phenotype. Further validation using a CRISPR/Cas9-mediated system confirmed that knockout of ClG42_04g0106300 results in the yellow-green phenotype in watermelon. In addition, comparative transcriptomic analysis revealed that the ClG42_04g0106300 mutations greatly affected the expression of key genes associated with chloroplast development and photosynthesis, providing strong evidence that it plays a critical role in these biological pathways. Taken together, these findings provide insights into the molecular mechanisms underlying chloroplast development and photosynthetic efficiency, offering a theoretical basis for breeding watermelon varieties with high photosynthetic efficiency.